Ben Clymer also scored twice, and Shaone Morrisonn added the other goal for the Capitals, who were 0-15-1 in their last 16 trips to Philadelphia.
Simon Gagne, Eric Meloche, and R.J. Umberger scored for the Flyers (3-9-1), off to one of the worst starts in franchise history.
The Capitals chased Flyers goaltender Robert Esche by scoring four times on eight shots in the opening period. Antero Niittymaki allowed one goal on 11 shots in relief.
Brent Johnson made 33 saves to earn his first win of the season.
Ovechkin put Washington ahead at 3:53 of the first period with a spinning shot after he picked up a loose puck in front of the crease.
Gagne tied it at 12:33 with a brilliant breakaway move, going forehand to backhand after skating the length of the ice.
The Capitals regained the lead for good at 12:59 when Clymer batted the puck in during a scramble. Washington then scored twice within 17 seconds. Morrisonn converted a long slap shot at 18:24 and Ovechkin finished off a 2-on-1 with Chris Clark at 19:01 to make it 4-1.
Clymer scored again off a rebound 29 seconds into the third period.
Meloche, playing in his first NHL game, scored on a one-timer for the Flyers at 6:40. Umberger cut the deficit to 5-3 with a power-play goal at 14:59.
Notes: Washington's previous win in Philadelphia was a 3-2 overtime decision on Jan. 31, 1998. ... Flyers C Randy Robitaille will be sidelined 7-to-10 after he sprained his left knee and ankle against Tampa Bay on Thursday. ... Ovechkin leads the Capitals with 16 points (eight goals, eight assists). ... The Flyers were 1-for-6 on the power play. They have the NHL's worst percentage, converting seven times in 80 chances (.088).