Andy McDonald had two goals and an assist, and Teemu Selanne added one of each to help the Pacific Division-leading Ducks avoid a four-game season sweep against the last-place team in the Northwest Division.
Joe Sakic, Mark Rycroft and Milan Hejduk scored for the Avalanche, who lost their third straight and 11th in 16 games.
Colorado's Karlis Skrastins, who injured a knee in Saturday's shootout loss to the Los Angeles Kings, had his NHL-record, consecutive-game streak among defenceman snapped at 495 games. He broke Tim Horton's mark nine games earlier.
Skrastins had not missed a game since Feb. 18, 2000, when he was with the Nashville Predators. Vancouver's Brendan Morrison now holds the league's longest current streak for any position at 492 games.
The Ducks, who came in averaging a league-leading 17.8 penalty minutes, received three penalties in the final nine minutes and were burned on the final one after Niedermayer was called for interference. Andrew Brunette threw the puck into the slot from the right boards and it skipped off the blade of Anaheim forward Samuel Pahlsson's stick before Hejduk backhanded his 24th goal past Jean-Sebastien Giguere.
Niedermayer redeemed himself less than two minutes later, beating Jose Theodore to the glove side with a screened wrist shot. Moments later, Hejduk received a four-minute high-sticking penalty after cutting McDonald, and Pronger capitalized.
After squandering a 2-0 margin, Anaheim took a 3-2 lead just 44 seconds before the second intermission. Selanne got a step on former Ducks defenceman Kurt Sauer and redirected McDonald's pass from the left boards for his 37th goal.
Rycroft trimmed Anaheim's lead to 2-1 at 18:15 of the first period. Sakic, playing in his 1,300th NHL regular-season game, tied it five minutes into the second with a power-play tally. It was Sakic's team-high 27th goal and 601st of his career, tying Jari Kurri for 16th place on the NHL list.
Only two minor penalties were called in the first period - both against Colorado defenceman Ken Klee. It took McDonald eight seconds into a power play to give the Ducks a 2-0 lead with his 18th goal and second of the game.
Notes: Skrastins was second in the league in blocked shots last season (207) and third this season (174). ... Colorado C Paul Stastny extended his point streak to 12 games with an assist on Hejduk's goal. It's the longest point streak by a rookie since 1992-93, when Selanne had a run during the final 17 games of the season with the Winnipeg Jets.