Toronto has now made five waiver moves since the end of the season with the main goal of continuing to build depth within the organization.
Herndon made five appearances for Philadelphia in 2012 while allowing four runs in 7 1/3 innings. In 97 Major League games, he has a 2-8 record with one save and a 3.85 ERA.
The 27-year-old underwent Tommy John surgery in June and is not expected to return until at least the middle of the year. He now joins a long list of Blue Jays who have recently suffered a similar fate, including Kyle Drabek, Drew Hutchison and Luis Perez.
Right-hander Tyson Brummett was designated for assignment to make room on the Blue Jays' 40-man roster. Brummett had been claimed off waivers from Philadelphia on Thursday.
The goal for some of these moves would be to potentially sneak players through waivers in the coming days and weeks. If Brummett does not get picked up by another club, he can be outrighted to the Minor Leagues and become a depth option at Triple-A Buffalo.