Paxton had allowed five hits and two runs with two strikeouts heading into the bottom of the fourth, but had to be taken out after throwing his first pitch of that inning.
The 26-year-old Canadian opened the season as Seattle's No. 2 starter and figured prominently in the Mariners' plans, but he was shut down on May 28 with a sprained middle finger on his throwing hand after going 3-3 with a 3.70 ERA in his first 10 starts.
Mariners manager Lloyd McClendon said prior to Paxton's Wednesday start that the plan was for him to throw 80-90 pitches.
"The biggest concern with Paxton is just making sure he comes through tonight healthy," McClendon said before the Mariners game against the Astros in Houston. "If he's healthy, he's going to be in the rotation when he comes back. That's a given."
Paxton is 12-7 with a 3.05 ERA in 27 career starts, but missed four months last year with a strained lat muscle behind his left shoulder and has missed more than three months this year with his finger injury.
Greg Johns is a reporter for MLB.com. Follow him on Twitter @GregJohnsMLB, read his Mariners Musings blog, and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.