The situation was so dire that manager Bruce Bochy used pitcher Noah Lowry as a pinch hitter in the eighth inning.
The shortage resulted because Rich Aurilia was available only in an extreme emergency after getting injections Monday to alleviate neck pain. And Ryan Klesko left for a pinch hitter in the fifth because of spasms in his back and hips.
Bochy had Barry Bonds in the on-deck circle to hit in the pitcher's spot, but sent Lowry up instead once Guillermo Rodriguez hit a sacrifice fly to leave the bases empty.
Lowry, a .192 career hitter, struck out.
Bochy also had Bengie Molina on the bench, but might have been gun-shy about using his backup catcher three days after an injury to Eliezer Alfonzo forced the manager to put infielder Pedro Feliz behind the plate.
"I wanted to keep Barry available in the ninth in case we got a runner or two on," Bochy said, adding he would have inserted Molina and moved Rodriguez to first base if the Giants had forced extra innings.
Bonds struck out against Jeremy Accardo with a runner at second base to end the game.
FIRST TIMERS: The Giants didn't get a sweep, but at least they got three milestones out of Wednesday's loss. Tim Lincecum, Jonathan Sanchez and Rodriguez each collected their first major league hits.
Lincecum, a rare right-handed pitcher who bats left-handed, called his swing "an ugly one" that resulted in a double down the left-field line. Sanchez was proud of his deep drive to the wall in left-center for a double.
Rodriguez toiled the longest for his run-scoring single in the fourth inning. The catcher spent 12 years in the minor leagues before making his major league debut Wednesday.
Rodriguez will be more thrilled when he throws out his first baserunner. He was 0-for-2 Wednesday, but the Blue Jays ran on a pitch in the dirt and another that Lincecum nearly threw over Rodriguez's head.
ONE-HOPPERS: Klesko said his back spasms might have stemmed from dehydration, and he expected to be available for Friday's game at Boston. ... Right-hander Vinnie Chulk left in the fifth inning after being struck on his right arm by a line drive. The bruise puffed up badly, but Chulk expected to be fine with a day of rest.