We have several pieces of evidence to say that Calvin affirmed the 66-book canon that has become known as the Protestant canon and rejected all other books as canonical.
The first piece of evidence is the 1559 French Confession of Faith, which he co-authored with De Chandieu. In article 3 of the confession, the 66 books are all named as "canonical" books of "the Holy Scriptures." In article 4 it says that "we can not found any articles of faith" upon "other ecclesiastical books."
Calvin names these "ecclesiastical books" in his 1547 Antidote to the Council of Trent:
It is well known what Jerome states as the common opinion of earlier times. And Ruffinus, speaking of the matter as not at all controverted, declares with Jerome that Ecclesiasticus, the Wisdom of Solomon, Tobit, Judith, and the history of the Maccabees, were called by the Fathers not canonical but ecclesiastical books, which might indeed be read to the people, but were not entitled to establish doctrine.
You may note that he mentions here every deuterocanonical book other than Baruch.
The next piece of evidence is the Geneva Bible, a 1560 English translation. David Hall makes the case that Calvin approved of the Geneva Bible:
Several things illustrate Calvin's imprimatur on this version. First, he used it in his own preaching; secondly, some of his closest disciples were involved in its translation; thirdly, publishings in Geneva at the time were approved by a committee of the Genevan Consistory, heavily populated by Calvin adherents; and fourthly, just prior to its publication, the church of Geneva requested that Calvin and Theodore Beza confirm William Whttingham’s NT translation. Without a doubt, Calvin approved of this 1560 translation.
In the table of contents of the 1560 edition, the deuterocanon (including Baruch) is in an "Apocrypha" section, and the Old and New Testaments include only the 66 books that Calvin affirmed in the 1559 French Confession (though the Prayer of Manasseh is listed with the Old Testament books with a note that it is apocryphal.)
Similarly, article 4 of the Belgic Confession lists the 66-book canon of Scripture, and article 6 enumerates the Apocrypha, including Baruch. Calvin wrote in a letter that he and the brothers of Geneva "heartily approve" of the Belgic Confession, which was written by a student of his, but wish it didn't attribute Hebrews to Paul. (A discussion of this letter is found in pages 67-70 of Nicolaas Gootjes' book The Belgic Confession, and the full text of the original is found in an appendix to the same.)
So to sum up, the evidence is as follows: Calvin's own French Confession of Faith, along with the Belgic Confession which his student wrote and he accepted, and the Geneva Bible which he also approved, names only the 66-book Protestant canon as canonical. And the Belgic Confession and Geneva Bible both explicitly regard each deuterocanonical book as non-canonical.
As for Baruch in particular, the webpage linked in the question gives examples of citations that are all from the 1530s -- though Calvin also calls Baruch a prophet in his 1546 commentary on 1 Corinthians -- which means he may have changed his mind between then and 1559 (possibly after 1547, since he doesn't mention Baruch in the Antidote to Trent). But an alternative would be that he's simply calling Baruch a prophet to give a common attribution that would be recognizable to his readers. This view makes more sense to me, given that a few of the passages mentioned by that webpage have Calvin saying, "Or whoever was the author." It seems he was simply adding weight to his arguments by quoting from an ancient Jewish writer.