Kevin Porter scored the lone goal for the Americans (30-25-10).
Rochester had an excellent chance at the equalizer with 2:55 remaining in the third.
Already on a power play, Marlies forward Sam Carrick was assessed a minor penalty for cross checking for his hit on Americans forward Johan Larsson. Rochester had a 52-second five-on-three power play, but failed to get a shot on goal.
Trevor Smith added an empty-netter with eight seconds remaining.
Americans starter Andrey Makarov made 33 saves in the loss, in his first AHL start.
The Marlies (39-20-5) have now won five of six and improve to 3-2-1 against Rochester this season with four meetings remaining in the season series.
Porter opened the scoring 57 seconds into the second period, walking around a Marlies defenceman and beating Sparks for his 15th of the season.
Abbott responded for Toronto taking Josh Leivo's wide shot and beating Markarov with a backhand shot for his 17th.
Rochester had a 1:10 two-man advantage just past the midway mark of the second period. Despite getting six shots on goal during the man advantage, the Americans could not beat Sparks.
McKegg gave Toronto its first lead of the afternoon beating Makarov with a floater at 18:37 of the second for his 16th.
Carter Ashton had an excellent chance to give Toronto a two-goal cushion three minutes into the third, but put his backhand shot off the crossbar.
The Americans trail the Marlies by 11 points in the AHL's North Division. Entering Tuesday, Rochester held a three-point lead on Charlotte for the eighth and final playoff spot in the Western Conference.
Toronto plays the second half of the home-and-home series with Rochester on Friday.