Hejduk broke a 1-1 tie at 6:57 of the final period when he took a pass from rookie Paul Stastny in the slot and beat Canuck goaltender Roberto Luongo with a hard shot to the stick side.
Stastny picked up his third assist of the game when Hejduk made it 3-1 during a scramble in front of the Canuck net at 10:54.
It was Vancouver's second loss in three games and prevented the Canucks from winning their second Northwest crown in three seasons.
The Minnesota Wild also used a 3-0 win over the Edmonton Oilers to inch to within one point of the Canucks in the race for the third seed in the Western Conference.
Defenceman Sami Salo scored Vancouver (48-25-7).
The Avs (43-30-7), are 14-1-2 in their last 17 games.
Colorado outshot Vancouver 30-18 and if it wasn't for Luongo the score could have been worse.
Luongo, who celebrated his 28th birthday Wednesday, played like an acrobat to keep the game close.
In the third period he got a pad on a Tyler Arnason shot and stopped a Joe Sakic backhand from in close.
In the second he got a glove on a Hejduk shot after the right-winger got in behind the Canuck defence during a power play. Later, a diving Luongo managed to get the shaft of his stick on the puck during a scramble in front of his net.
The Avs took a 1-0 lead just 25 seconds into the game while many in the sellout crowd of 18,630 were still looking for their seats. Hejduk picked up a loose puck, stickhandled between defencemen Willie Mitchell and Kevin Bieksa, then beat Luongo with a hard shot to the stick side.
The Canucks thought they had scored goals 26 seconds apart in the first period but only one counted.
Markus Naslund appeared to have tied the game at 7:33 when the puck hit his skate and went into the net. The goal was disallowed when the video replay judge ruled it had been kicked in, a questionable call that produced boos from the crowd.
Salo finally tied the score at 7:59 when his shot from the point appeared to be deflected past Peter Budaj.
During the game the Canucks announced their team awards. Not surprisingly, fans voted Luongo as both the most valuable and exciting player. Bieksa was chosen best defenceman and unsung hero.
Notes: Defenceman Rory Fitzpatrick was relegated to the press box due to Mattias Ohlund returning after missing four games with an elbow injury. . . . It was fan appreciation night with Canuck players giving selected fans their jerseys after the game. . . . Vancouver wraps up its season with games in San Jose Saturday and Phoenix Sunday.