Glavine was injured while throwing a pitch in the top of the inning. He completed the inning, throwing 18 pitches -- 11 for strikes -- and was replaced by Dan Wheeler to start the second.
Glavine is listed as day to day.
The Brewers loaded the bases in the first against Glavine, who allowed two hits. Brady Clark reached on catcher's interference with two outs, but Glavine got Keith Ginter to line out, ending the threat.
This injury is the latest in a season of misfortunes for Glavine, who is in his first year with the Mets. He is 6-11 with a 5.10 ERA and has only one win in his last 12 starts.
It was Glavine's second one-inning stint this season -- both at home against Milwaukee. On June 5, Glavine was forced out because of swelling in his left elbow. That was his shortest outing since May 16, 1989, at Chicago, when he didn't retire a batter.
Glavine was forced to leave in the sixth against the Yankees on June 22 because of a tight abdominal muscle. That was caused when the former Atlanta Braves ace was struck in the chest by a ball hit by Derek Jeter.