"When he was on the ground, I knew something was bad," Marlins manager Ozzie Guillen said. "I just saw it right away. Same thumb. Same injury. I don't expect him back this year."
A tearful Bonifacio had an X-ray taken after the game, and the Marlins hardly celebrated an otherwise inspiring victory, where Josh Johnson struck out nine in 8 2/3 innings.
Bonifacio added an RBI single and stole his 30th base, in the eighth inning off Gio Gonzalez.
"I think this kid is the glue of the team," Guillen said. "You can see a lot of long faces out there. I'm very happy we win. We pitched well. We put up a very nice inning together, against Gio, it's not an easy thing to do. JJ was outstanding. He did a very good job."
Bonifacio initially injured the thumb on May 18 at Cleveland. He tore ligaments in the thumb, jamming it on the base while being caught stealing.
He was on the disabled list from May 20 until July 13.
The injury on Friday came while Bonifacio was attempting a diving, backhanded attempt on Michael Morse's two-out single in the ninth inning off Johnson.
Bonifacio actually reached the ball, knocked it down, and collected it. But in pain, he flipped the ball to shortstop Jose Reyes, who wasn't anticipating the ball. As it drifted away, Bryce Harper, who singled to open the inning, scored from third.
The Nationals scored their second run, which was unearned, and Johnson was relieved by Steve Cishek, who logged the one-out save.
The Marlins are expected to select the contract of Nick Green from Triple-A New Orleans on Saturday.
For the season, Bonifacio is batting .261 in 61 games.
He opened the season in center field, but moved to second base after Omar Infante was traded to the Tigers.
"Now, our game changes," Guillen said. "I've got to figure out a lot of things."