It was the eighth win in a row against Toronto overall.
Florida right-hander Josh Johnson pitched a seven-hitter for his second complete game of the season.
Paulino went 4 for 5, scoring three runs and driving in three with his first career multihomer game. He hit a two-run drive in the second inning and added a solo shot in the ninth.
"He's the star of the game right there," Johnson said of Paulino. "I pretty much just follow him. We're always on the same page and, if we're not, he pretty much goes right to what I'm thinking."
The sweep got the Marlins (32-33) back to within one game of .500 as they prepare for a three-game series at Boston on Tuesday. After that, it's home to face the New York Yankees and Baltimore before wrapping up interleague play with three games at Tampa Bay.
