The Giants can ill afford to lose Nunez for any length of time as the regular season's final week approaches and the National League Wild Card race intensifies.
"That's something we don't need now, to be honest," Giants manager Bruce Bochy said.
Nunez is batting .338 (25-for-74) with 10 runs scored and 10 RBIs in his last 19 games.
"There's something there," Nunez said. "I'm hoping to play Tuesday. But we'll see [Monday] what's going on."
Nunez said he felt something wrong as he took his final step before he slid.
"I thought it was a cramp," he said, though he knew better when he stood up. Nunez left the game immediately and was replaced as a runner by Gregor Blanco. Ehire Adrianza stepped in for Nunez at third base.
Nunez, 29, said he never has encountered extreme hamstring problems.
"Sometimes they get a little tight, but nothing where I missed four to six weeks."
San Francisco's other ailing infielder, shortstop Brandon Crawford, returned to the lineup and went 0-for-3 with a walk. Crawford, who missed four games after dislocating his left pinkie Tuesday at Los Angeles, participated in turning three double plays.