Ottawa's Kyle Turris appeared to have broken a 2-2 tie 9:30 into the third period when his shot from the slot hit the skate of Flyers defenseman Nicklas Grossmann behind the goal line.
But the on-ice officials waved it off and a video review upheld the decision.
Only 2 minutes later, Kimonen put Philadelphia on top with a shot through the pads of Robin Lehner and Wayne Simmonds quickly notched another goal to put the Flyers in control.
Turris scored earlier in the final period and Clarke MacArthur added a goal and an assist for the Sens, who dropped a third in four contests.
Lehner finished with 37 saves.