Hamrlik scored off a faceoff with 6:11 left in the third period to snap a tie and the Flames defeated the Blackhawks 3-2 for their third straight win.
After Wayne Primeau won a draw in the Chicago zone, Hamrlik beat Khabibulin on the short side with a drive from the left point. Hamrlik was able to tee up the puck after it was ticked into perfect position by Calgary's Matthew Lombardi.
Moments earlier, Khabibulin had been hit in the mask by Phaneuf's high shot. Play was stopped, setting up the faceoff.
"That was a good shot from Dion, too," Hamrlik said, noting that it might have shaken up Khabibulin.
Hamrlik then netted the winner with a blast that sailed past Khabibulin on the stick side.
"It was right in front of me and there was no reason to pass," Hamrlik said. "Nothing is better for a defenceman. That was a perfect setup."
Khabibulin wasn't available to comment after the game. However, Chicago coach Denis Savard said Phaneuf's shot might have affected his goalie.
"That could have had something to do with it," Savard said. "I'm not sure. He wasn't screened."
Kristian Huselius and Stephane Yelle also scored for the Flames. Calgary has 90 points and strengthened its hold on the eighth and final playoff berth in the Western Conference.
"We don't care who scores," Hamrlik said. "It was a big win, a huge two points."
The victory also launched a four-game road trip for the Flames, who are 10-18-8 away from Calgary.
"This was a really important win to start our road trip," Flames coach Jim Playfair said. "Besides the first period, I thought we did a lot of things right."
Radim Vrbata and Denis Arkhipov scored for Chicago, which lost its fifth straight despite leading 2-1 after two periods.
"We've got a young team, young players that are learning, including myself," Chicago defenceman Duncan Keith said. "It's important for us to kind of buckle down in the third period and find a way to win some of these games."
The Blackhawks are in 14th place in the West and have been eliminated from playoff contention for the eighth time in nine seasons.
Khabibulin stopped 27 shots. Calgary's Miikka Kiprusoff made 29 saves.
Martin Havlat, Chicago's leading scorer, was held without a goal for the 12th straight game. He has five assists during the slump.
Huselius opened the scoring 2:01 into the first when he beat Khabibulin on the short side from the left circle.
Vrbata tied it at 5:55, when he skated unchallenged out of the left corner and stuffed a shot under Kiprusoff's pads.
Arkhipov gave Chicago a 2-1 lead on a deflection with 5:59 left in the first. While cutting through the right circle, he redirected Brent Seabrook's drive from the point.
Yelle's goalmouth deflection tied it just 48 seconds into the third. Among several players screening Khabibulin, Yelle tipped in Phaneuf's low drive from the top of the slot.
Notes: Calgary LW David Moss missed his fourth game with a lower body injury. Flames D Mark Giordano, D Andrei Zyuzin and RW Eric Goddard were healthy scratches. ... Chicago C Peter Bondra returned after missing four games with a shoulder injury. ... Blackhawks LW Tony Salmelainen and RW Nikita Alexeev were healthy scratches.