The Giants made the move before Friday night's game against the Colorado Rockies.
On Thursday, Affeldt did not retire any of the four hitters he faced against the San Diego Padres.
Giants manager Bruce Bochy said it was a gradual thing and Affeldt has been battling it for a while.
Right-hander Mike Broadway was recalled from Triple-A Sacramento to take Affledt's place on the 25-man roster.
Giants outfielder Angel Pagan was to get an MRI on his bruised left knee and was not in the starting lineup.