Price retired the first two hitters he faced before Astros outfielder Michael Brantley singled Saturday. Rookie right-hander Colten Brewer replaced Price on the mound.
Red Sox manager Alex Cora said Price had been battling the flu for four days.
"We were proactive," Cora told the Fox TV broadcast. "We took him out of the game, he'll get some treatment, and we'll see what happens."
Brewer pitched 2 1/3 scoreless innings after entering the game.
Price recently battled elbow tendinitis. The five-time All-Star is 2-2 with a 3.24 ERA in eight starts this season.
The Red Sox fell to 27-25 with Saturday's loss. Boston trails the rival Yankees by 7 1/2 games for first place in the AL East Division.