Marquis took a line drive to the palm on his glove hand in the second inning against the Pirates. He was able to knock down Pedro Alvarez's ball and complete a throw to first base for the out.
The Padres' training staff attended to Marquis, as did manager Bud Black, though he remained in the game.
"I had an idea it could possibly be broken," said Marquis, who pitched 5 1/3 innings in a no-decision. "... But you have to drag me off the mound."
Marquis, who is 6-7 with a 4.04 ERA in 15 starts with the Padres, had an X-ray on his hand late Tuesday that was negative. However, a CT scan Wednesday afternoon revealed a fracture of the bone located at the base of the thumb.
Black said he was unaware of the fracture until he was told in the eighth inning of the Padres' 4-2 victory over the Pirates on Wednesday.
"The CT scan showed some action," Black said. "We're going to look at it and determine what we're going to do."
Marquis isn't scheduled to pitch again until Monday when the Padres open a three-game series against the Braves at Petco Park.
"We'll let the swelling subside and see what happens," Marquis said. "I want to be on the mound. I will keep my arm in shape and then we'll decide what to do."