The hearing took place in St. Petersburg, and a ruling could come as early as Wednesday.
Bonifacio is seeking $2.2 million, while the Marlins have countered with $1.95 million.
The Marlins opted to go to a hearing with Bonifacio because, per team policy, they let an arbitration panel decide a player's salary if an agreement isn't reached by the salary exchange deadline.
Jan. 17 was the deadline, and the Marlins were unable to come to terms with Bonifacio and Anibal Sanchez.
Sanchez had his hearing in St. Petersburg on Friday and the panel ruled in favor the right-hander on Monday. The 28-year-old will make $8 million this season, instead of the $6.9 million the Marlins offered.
Bonifacio, who made $425,000 last year, is in his first year of being arbitration-eligible.
The 26-year-old enjoyed a breakout season in 2011. He appeared in 152 games, batting .292 with a .360 on-base percentage. He added 40 stolen bases. In July, he batted .380 and was named the National League Player of the Month. He also had a 26-game hitting streak.
After the All-Star break, Bonifacio hit at a .305 clip, with 24 steals.
Formerly a super utility player, Bonifacio projects to be the starting center fielder. But that could change, depending on the health at other positions.
Hanley Ramirez is coming off left shoulder surgery, and the three-time All-Star is expected to be ready for the season opener. If he isn't, Bonifacio could be an option at third base.
Bonifacio is also an option to play shortstop or second base, as well as all three outfield positions.