The same thumb required surgery on May 25 to repair a torn ligament.
This time, the Marlins are wondering if the speedster is done for the season. Perhaps there is hope for a return in two or three weeks.
"Wait and see," Marlins general manager Michael Hill said. "Obviously, you don't want to speculate until he has time to see the doctor. He got an X-ray here, which was negative."
Bonifacio re-injured his thumb in the ninth inning of Game 2 of Friday night's doubleheader at Nationals Park.
"He's going to be out 15 days and hopefully no more than that," manager Ozzie Guillen said. "Then we're going by ear.
"When I saw it, to me, I thought he was out for the season. The way he was reacting and the pain. We don't know yet. The X-rays came back negative."
Replacing Bonifacio on the roster is infielder Nick Green, who had his contract selected from Triple-A New Orleans.
Guillen says Bonifacio is one of his toughest players to replace.
"This kid is the soul of this ballclub," Guillen said. "This kid can bring a lot of great things to this ballclub -- not only on the field, but off the field. He's liked by his teammates, the way he goes about his business. Hopefully it's just a few weeks."
Bonifacio opened the season in center field, and he moved to second base when Omar Infante was traded to the Tigers in late July.
In 61 games, he was hitting .261 with 30 stolen bases. He had been leading off since Jose Reyes moved into the third spot.
Bonifacio initially jammed the thumb on May 18 in Cleveland. Two days later, he was placed on the DL.
When he had surgery, a couple of pins were inserted to stabilize the area. Why Miami is holding out hope that Bonifacio may return is because there is not believed to be any further structural damage.
"X-rays showed everything was what it was," Guillen said. "The pins, they were in the same place. Maybe he just strained the ligament. You can put it that way. That's what they told me."
The Marlins reinstated Bonifacio on July 13, the first game after the All-Star break. He had been wearing a protective guard while running the bases. But he didn't have any extra padding in the field.
Bonifacio was injured trying to make a diving play on Michael Morse's grounder up the middle.
The 33-year-old Green is a utility infielder who was with the club in Spring Training. He's enjoyed a strong season at New Orleans, batting .344 with 16 doubles, 12 home runs and 47 RBIs in 63 games.
New Orleans immediately lifted Green from its game at Salt Lake City on Friday night once it was learned Bonifacio sprained his thumb.
Green has played in parts of six big leagues seasons. His last stint was with Toronto in 2010. He provides depth at third base, shortstop and second base.
Miami's infield is short because Donnie Murphy could miss at least a few games with a left hamstring strain.
"Obviously, I'm willing to play wherever and do whatever they ask me to do," Green said. "Hopefully the guys can finish off strong. ... There is still something to gain from the season. If you can push through, it shows a lot of character for who's here. Hopefully we can do that."