The Padres pinch-hit for Hudson in fifth inning at Citi Field, one inning after he drove in a run with a double to center field.
Hudson was replaced at second base by Alberto Gonzalez.
San Diego manager Bud Black said that it was too soon to tell the severity of the Hudson's groin strain.
"We're going to look at it tomorrow to see how it sets up," Black said.
Hudson has been on the disabled list twice this season. He missed 13 games May 4-19 with a strained right hamstring. In May, Hudson missed 22 games with a strained left groin, and injury that sidelined him from May 27 to June 19.
Hudson entered Tuesday hitting .239 with three home runs and 27 RBIs for the Padres.