Jaromir Jagr scored two power-play goals and Scott Hartnell tied it with 3:02 left in regulation for the Flyers, who trailed 3-0 late in the second period. Ilya Bryzgalov made 19 saves in Philadelphia's return from a five-day break.
Teemu Selanne and Andrew Cogliano scored first-period goals and Jonas Hiller stopped 43 shots for the Ducks, who lost for the 17th time in 20 games. Anaheim couldn't maintain its fast start under Boudreau, who replaced Randy Carlyle late Wednesday night after getting fired by Washington on Monday morning.
Philadelphia got a four-minute power play in overtime when Ducks captain Ryan Getzlaf committed a hooking penalty and then slammed his stick on the glass in anger, earning another unsportsmanlike-conduct minor. Anaheim killed 2:37 of the penalties, but Giroux was left alone to score on a one-timer from Daniel Briere.
Saku Koivu had two first-period assists for the Ducks, who have lost eight of nine.
In their first time back on the Honda Center ice since Carlyle's firing after six-plus seasons, the Ducks clearly aimed to impress their new coach, playing with all the energy and nastiness they've lacked far too often this season. Boudreau also learned Anaheim hasn't shaken its propensity for needless penalties, repeatedly putting the Flyers on power plays.
After Jagr scored twice, Hartnell tied it with a close-range goal off a pass from Kimmo Timonen, who assisted on all three regulation Flyers goals.
Boudreau took over after the Ducks got off to a 7-13-4 start, falling to 14th place in the Western Conference despite a wealth of talent. Boudreau led the Capitals to four consecutive Southeast Division titles and the 2010 Presidents' Trophy while winning 200 games faster than any coach in NHL history.
The Ducks took the lead early when Koivu fired a lead pass to Cogliano, who slipped the puck underneath Bryzgalov with a change-of-pace shot. Cogliano has been one of the few bright spots of his first season in Anaheim, scoring six goals while earning a spot on a line with Selanne and Koivu.
Selanne then added his ninth of the season on a one-timer from Koivu midway through the period. Anaheim's physical play included vicious hits by Francois Beauchemin and Matt Beleskey in the first period, the Ducks showing a passion they've often lacked this season.
Gordon, who played for Boudreau in Washington last season, then scored his first goal in his 25-game tenure with the Ducks, batting home a rebound of Ben Maxwell's shot.
Jagr redirected Timonen's shot in front of Hiller on the power play for the Flyers' first goal. Jagr missed four of the previous five games with an apparent groin injury, but returned for his first goal since Nov. 5.
Jagr then scored with 5 seconds left on a two-man advantage early in the third period for his third two-goal game since rejoining the NHL this season.
NOTES: Before the game, Boudreau added assistant coach Bob Woods and video coordinator Joe Piscotty to his staff. Woods had been on Boudreau's staff in Washington since 2009. ... Gordon's goal was the second of his NHL career. ... The Flyers scratched D Matt Walker after recalling him from the AHL earlier Friday. ... Flyers D Chris Pronger still hasn't played at Honda Center since the Ducks traded him to Philadelphia in June 2009. Pronger, who won the Stanley Cup with Anaheim in 2007, could be out for a month after knee surgery on Tuesday. The 2000 NHL MVP and current Flyers captain also missed Philadelphia's last game in Anaheim on Dec. 31, 2010, while recovering from foot surgery.