Hernandez exited Friday after throwing 31 pitches for Triple-A Tacoma. The Mariners said Hernandez came out of the game when he wore down, not because of pain.
Hernandez gave up two hits and two runs in 2⅓ innings against San Antonio before coming out. He struck out two and walked one.
Seattle had hoped its former ace would throw between 50-60 pitches in his first outing since going on the injured list because of right shoulder stiffness on May 12.
The 33-year-old right-hander is 1-4 with a 6.52 ERA in eight starts for Seattle.