It might be worth a bit more understanding of how it is that the books of the Apocrypha are not considered part of the Bible by Protestants. It has as much to do with accidents of history as it does with theology.
As SeventhValley writes above, these books were included in the Septuagint (LXX). The LXX was a Greek translation of the Hebrew scriptures, and was in essence the Bible for the first generation of the Christian Church. When Paul wrote to Timothy that all scripture was God-breathed, he was referring to this collection of scriptures, because he was writing to a Greek-speaking community. That Paul himself used the LXX is something we can see because there are a few differences in the LXX and the Hebrew forms of the Old Testament, and Paul's quotations of OT often reflect these variations.
So, the NT church, even the NT writers made use of the LXX as their Bible. And for the next 1500 years whenever the church considered what was scripture, these books we today know as the Apocrypha were considered a part of it. So, how did they get excluded?
Well, that has to do with the whole idea of how we formed canon.
The NT Church never really worried about the idea of what was and was not canon. They didn't, because the Jews never really had. What they had was the Law and the Prophets and Writings. They were very careful with preserving these books, but they were not so careful and identifying different levels of acceptability among them. If you were a Sadducee you accepted only the first five books identified with Moses, the Pentateuch, or Torah. But the scribes and Pharisees would accept all of the Prophets and other writings (such a the Psalms and Proverbs) as well. So, when the Maccabees, or Tobit was written these were accepted too. But other groups, such as the Essenes had their own preferred collections, often with books they had written themselves and weren't in circulations outside of their circle. This is because the Jews had no set canon. The idea of having an established canon was something that developed within the Church in the 2nd and 3rd centuries.
Actually, like the Jews before them, the early church had different collections of scriptures depending on various factors: geography, influence of particular church Fathers, and most importantly what they had access to. You see, we think of the Bible as a bound book. But that is not what the Bible actually is. The Bible is NOT a book. The Bible is a library, a collection of books. )Even the word for Bible in other languages is related to this concept of library, for instance in Spanish they are Biblia & biblioteca). And for the first couple hundred years of the church these individuals books were each on their own scroll, just like they had been kept that way by the Jews. (Trivia: some books like Samuel were so long as to require 2 scrolls, hence we have a 1st & 2nd Samuel; others like what we call the Minor Prophets of Hosea thru Malachi were so short as to be written on one scroll. But on the whole each book had its own scroll.) And, being precious writings, they were all safely kept in one place. As other writings were received, be they letters or novels, they too were kept with the other scrolls. And then the codex, the earliest from of a book, was invented. It was a piece of high tech engineering that enabled people to keep all that was written on their unwieldy scrolls in one easy and convenient to carry place.
But when downloading from the scrolls into these codices, what should and what should not be kept together? The was such an important question in the 2nd and 3rd centuries of the Church that they actually convened church councils to make the decision. These council were to establish canon. Now, in fact, the councils did not vote on what the canon would and would not be, that was a process that had been going on in the church over the centuries. What the councils did was recognize what in time had become the accepted canon of the church in actual practice. But, it did take time to get there. In the end they recognized the 27 books of the NT that we presently have and the Hebrew scriptures. The only problem with that is that the Jews themselves had not yet actually established any canonical list of accepted books of Hebrew scriptures in the same way that the Christian church had done with the New Testament. Greek-speaking Jews used the LXX (including books like Tobit and the books of the Maccabees) now written on codices, while Hebrew-speaking Jews were still using their collection of scrolls. Since by now most Christians were Greek-speakers, the LXX was simply adopted as the OT for the church. And when the Bible was translated into Latin, copies of the Greek LXX codices (not the Hebrew scrolls) were what was used as the text to translate the OT into Latin.
For the next 1000 years the Church just copied these Latin translations. Then comes Luther.
Now, Luther was not the first to translate the Bible into common language, after all that was the whole purpose of the Latin Vulgate -- to get a copy of the Bible in the common language of the people of its day -- and there had been a few isolated instances in the century before Luther. But he would do it about the time that the printing press was invented and when the laity were finally becoming educated enough that at least the rich were themselves learning to read. In addition, Luther did it for a group of people that were rejecting all things Catholic, and that would include the last 1500 years in the history of our sacred writings. His translation would become a standard for Protestant Christians for centuries to come, but not so much for the translation itself as much as for the methodology.
What Luther did was decide not to translate the inherited Latin text into German, but from the original languages. This was no easy task in Luther's day. First, most ancient texts where held by the Catholic church, a group he couldn't go to for help. Second, even the Catholic church hadn't kept the original Hebrew, because they had never used it. The early church being Greek-speaking and having a copy of the OT in Greek already in the form of the LXX, they simply continued to maintain what they already had as I've already described above. So, where will Luther turn for a Hebrew text of the OT? The answer was as close as the Jewish communities in Germany.
However, Judaism had changed in the last thousand years. The nascent Christian community that had adopted the LXX as its own did not stay the small non-threatening offshoot it had once been. It grew, and it began to be a threat to Judaism. You can see that as early as the conflict recorded in Acts 15. But it would become more so when these Christians began to use the very scriptures the Jews themselves used to declare that this man Jesus that the Christians worshiped was in fact not just the Jewish Messiah (there had been hundreds before of mostly little significance) but actually God incarnate. And some of the places that they got these ideas from where in particular Judith and Tobit. So, the rabbis decided that they needed a more defined canon as well, and the process by which that canon was determined coincidentally would exclude those books that Christians had found so helpful to their cause.
Thus by the time Luther is asking the rabbis of Germany for a Hebrew copy of the Bible, it does not include some of the books found in the Latin editions of the Bible (or even the Greek editions of the OT if he had had access to them). In the end Luther settles on the same 39 books of the OT that we have today, and the 27 books of the NT that the church had settled on early in its own history, this list gets passed into the understanding of what it means to be protesting the corruption of the Catholic church at the heart of the Reformation, and the rest is history.