Herndon, a right-hander, missed most off the 2012 season after undergoing Tommy John surgery in June. The 27-year-old pitched in only five games, going 0-1 with a 4.70 ERA, before landing on the disabled list with right elbow inflammation on April 30.
He spent 2010 and 2011 in the Phillies' bullpen, going a combined 2-7 with a 3.79 ERA over 92 appearances.
Herndon is expected to make a midseason return from his injury. To make room for him on their 40-man roster, the Blue Jays designated right-hander Tyson Brummett for assignment. Toronto claimed Brummett off waivers from Philadelphia on Thursday.
The Phillies also announced that Kevin Jordan, a Minor League coach who spent 2012 with the Gulf Coast League Phillies, opted to not return for the 2013 season.
Jake Kaplan is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.