Before leaving the game, Morse was 0-for-1 with a strikeout. He was replaced in the bottom of the fourth inning, when Roger Bernadina came in as a pinch-hitter and popped up to Cubs second baseman Darwin Barney.
Morse didn't want to come out of the game, but he was overruled by manager Davey Johnson.
"I heard late that he complained to the trainer," Johnson said about Morse. "Even though I talked to him about it, he said the thumb was good. I said, 'No, you're done.' With the night off and a full day tomorrow, he should be OK."
Morse said the thumb is OK and he expects to play Tuesday against the Cubs.
"My hand feels fine. My hand feels fit," Morse said.
The injury dates back to last month, when he was hit by a pitch against the Giants.
Morse started the season on the disabled list because of a strained right lat and missed the first two months with the injury.
He entered Monday's series opener batting .289 with 12 homers and 47 RBIs for the Nats in 2012.
Bill Ladson is a reporter for MLB.com and writes an MLBlog, All Nats All the time. He also could be found on Twitter @WashingNats. This story was not subject to the approval of Major League Baseball or its clubs.