After Game 1 of Wednesday's doubleheader at Arizona, the Marlins placed Bonifacio on the 15-day DL with a right knee sprain. Previously, he spent two stints on the DL with a sprained left thumb.
Manager Ozzie Guillen says the ailment shouldn't require surgery, but the chance remains that Bonifacio could miss the remainder of the season.
"If we're not going anywhere, why are we going to take a chance for him to get hurt again, to go to Minor League rehab and do all kinds of stuff to come back?" Guillen said. "To me, it's up to him. But why risk something that shouldn't be risked?"
Replacing Bonifacio on the roster was lefty reliever Dan Jennings, who was recalled from Triple-A New Orleans. Jennings was sent back down after the doubleheader nightcap.
Something didn't feel right in the first inning on Tuesday night when Bonifacio planted and threw the ball to third base. He was lifted an inning later for pinch-hitter Gorkys Hernandez.
On Wednesday morning, Bonifacio had an MRI on his knee, and the results confirmed the sprain but showed no serious damage.
"It started bothering me when I made the first throw to third," said Bonifacio, who is holding out hope he can return.
The D-backs scored five runs in the first inning on Tuesday in Miami's 6-5 comeback win. The play that caused the problem for Bonifacio was on Jason Kubel's single to center. As Aaron Hill headed to third base, Bonifacio's knee buckled when he set and threw to third.
Bonifacio stayed in the game and caught two fly balls in the inning. Upon returning to the dugout, Bonifacio said his knee was bothering him and was replaced by Hernandez.
"I never felt that with my knee [before]," Bonifacio said. "It was a concern. I couldn't step real hard. That was my concern."
Speed is a huge part of Bonifacio's game. He's one of the fastest players in baseball, and he has been used in the leadoff spot. He is batting .258 with a .330 on-base percentage and has 30 steals.
But it's been an injury plagued season for the 27-year-old. He was reinstated from the disabled list Sunday after being out with a sprained left thumb since Aug. 3. The injury occurred when he made a diving attempt at a ground ball while playing second base against Washington.
Bonifacio initially injured his thumb on May 18, tearing a ligament. He had surgery on May 25 and was out until the All-Star break.
The Marlins moved Bonifacio back to center field upon his latest return from the DL to avoid further problems with his thumb.