The speedster is confident he will not need more than 15 days to recover.
"They are being careful, they don't want it to be worse," said Bonifacio, who has his thumb supported by a brace. "They just want to make sure."
The decision came a day after an MRI revealed no fracture to Bonifacio's thumb, which was jammed while he was attempting to steal second base on Friday night. Bonifacio was caught stealing for the first time this year when he was thrown out by Cleveland catcher Carlos Santana in the fifth inning.
One of the fastest players in the league, Bonifacio is hitting .268 with a .351 on-base percentage. He set the franchise record with 21 straight successful steals before he was tossed out on Friday.
Bonifacio, who used a head-first slide, jammed his thumb on second base.
The Marlins, on Sunday, recalled outfielder Chris Coghlan and selected the contract of infielder Donovan Solano. Both are getting the call up from Triple-A New Orleans.
Coghlan, who was on Miami's Opening Day roster, was optioned to New Orleans on April 29. In 16 games with the Zephyrs, he batted .275 with six doubles and seven RBIs.
The 2009 National League Rookie of the Year Award winner was used in a limited role off the bench for Miami early in the first month of the season. He saw action in 19 games and was hitting .118 (4-for-34) at the time he was sent down.
"I feel myself again," Coghlan said. "I went down, and the first four or five games, I was trying to get my timing back. And getting in the swing of playing every day. I was grateful I got to play every day. In probably my last 10 days down there, I was back to my old self. Enjoying being in that mode and that mindset."
Coghlan provides outfield depth, and he is an option to play center field. Bryan Petersen also is a choice to play center until Bonifacio returns.
With Logan Morrison expected to receive playing time at first base now that Gaby Sanchez has been optioned to Triple-A, Coghlan could see time against right-handed pitchers in left field. Austin Kearns also is expected to play in left field, especially against lefties.
Solano, a 24-year-old from Colombia, was signed as a non-drafted free agent by the Cardinals in 2005. This is the first time he has been called up to the big leagues.
Signed to a Minor League contract with an invitation to Marlins' Spring Training, the infielder impressed manager Ozzie Guillen and the staff in the spring.
In 36 games with the Zephyrs, he batted .262 with seven doubles, a triple and 14 RBIs.
Solano has been hot lately, going 8-for-19 while riding a five-game hitting streak.
"This is very exciting," said Solano, whose hero growing up in Colombia was Edgar Renteria. "I wasn't thinking about this opportunity coming this soon. I'm so excited. My family. My brother. My mom. Everyone is so excited right now."
Solano becomes the 12th player from Colombia to reach the big leagues.
"Right now, everybody there is talking about me being one more Colombian making it to the big leagues," Solano said. "It's big there right now. Everybody is happy over there."