Bundy was supposed to make his third appearance Monday but was pulled because of the injury, according to Orioles executive vice president Dan Duquette.
Bundy has been fighting injuries since the Orioles made him the fourth overall pick in the 2011 draft.
He underwent elbow ligament replacement surgery in 2013 and was shut down this season in May with shoulder inflammation.
Bundy's only stint in the majors came in 2012, when he pitched two games out of the bullpen for Baltimore.
The right-hander made two one-inning fall league appearances before Monday, throwing a total of 26 pitches.