The team recalled right-handed pitcher Ryan Webb from Triple-A Portland to take the place of Gallagher on the 25-man roster.
Webb was in uniform for Tuesday's game and prepared to pitch against the Rockies if needed.
Gallagher has a 6.92 ERA in nine games this season. He threw 1 2/3 shutout innings in the Padres' 5-2 loss to the Rockies on Monday.
But the pain in a toe that he stubbed in a hotel room late last month in Cincinnati never healed.
"I just caught it square," Gallagher said. "It just hasn't gotten any better."
Gallagher has struggled in long relief this season, allowing 14 hits and 13 walks over 13 innings. Opposing batters are hitting .292 against him.
Webb hasn't allowed a run in nine games this season with Portland. He's struck out 10 batters in 10 innings and opponents are batting .172 against him. Webb hasn't appeared in a game since April 30, so he should be available to pitch Tuesday.
Webb was sent down fairly early in Spring Training in large part so that he could work on a new delivery at the urging of Padres pitching coach Darren Balsley.
"Before I was over the top, and now I've dropped my arm angle. It's added more deception," Webb said. "From what I can see, I'm keeping the ball down in the zone and getting a lot more ground balls."
Oddly enough, Webb and Gallagher were obtained from the Oakland A's in the same deal on July 5, 2009. In that deal, the Padres sent outfielder Scott Hairston -- who has since been reacquired -- to the A's for Webb and Minor League reliever Craig Italiano.
Gallagher was the player to be named later in that trade.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.