Alex Ponikarovsky, Matt Stajan, Mats Sundin and Darcy Tucker scored for the Leafs, who dropped to 29th overall in the 30-team NHL after Tampa Bay beat Philadelphia on Thursday night.
The Leafs are eight points out of a playoff spot in the Eastern Conference with 23 games to play in the regular season and have five games left before the Feb. 26 trade deadline.
Rick DiPietro made 27 saves for the Islanders while Vesa Toskala stopped 24 of 28 shots.
Berard opened the scoring on a power play with 3:48 to go in the first period, busting into the slot and redirecting a Miroslav Satan pass past Toskala.
Tucker got credit for the tying goal at 7:51 of the second period. Stajan's pass toward the slot deflected off both Tucker and Isles defenseman Aaron Johnson and skidded between DiPietro's legs.
Sundin later slid in a rebound to give Toronto its only lead of the game.
But then the Isles' power play went to work as the Leafs took three consecutive penalties, Fedotenko tied it 2-2 at 14:36 when he banged in a puck that was sitting on the goal line after Josef Vasicek hit the post.
Comrie, with his 17th of the season, put the Isles back in front 3-2 with a power-play goal at 17:25 when he took Satan's nifty pass across the slot and slid it an inch past the goal line under Toskala.
The Isles took a 4-2 lead 4:29 into the third period when Fedotenko scored a nearly identical goal to his first one of the game, banging home a puck in the crease behind Toskala on yet another New York man advantage.
The Leafs rallied. Stajan scored his team's third goal on a Toronto power play at 10:16. The Leafs had a chance to tie it on a two-man advantage just moments later, but couldn't deliver the tying goal.
Meyer, with his first goal of the season, scored in the empty net with 51.5 seconds to make it 5-3. But Ponikarovsky pounced on a rebound in the slot with 18.3 seconds left to cut the lead to one goal again.
Toronto went 1-for-4 with the man advantage while the Islanders went 4-for-7.
