Leading 1-0 in the second period, Michalek delivered a critical blow with a shorthanded goal at 7:33.
With Calgary deploying four forwards on the power-play as coach Mike Keenan often will do, it backfired when Alex Tanguay mishandled the puck at the Sharks blue-line enabling Michalek to break away down the wing.
As the Flames' Dion Phaneuf came across in pursuit, Michalek's fired a shot that Kiprusoff stopped, but he kicked out the rebound right onto Michalek's stick and he fired it into the open side beyond Kiprusoff's outstretched pad.
Michalek added his second of the night and sixth of the night in the third on a pretty set-up by Jeremy Roenick from behind the net.
Ryan Clowe and Steve Bernier also scored for San Jose (5-3-1). The Sharks began a four-game road trip that continues Friday night in Detroit.
Daymond Langkow with his eighth goal of the season accounted for the lone goal for Calgary (4-3-2). The Flames suffer their first regulation loss in six games (4-1-1).
Until Langkow's goal with 3:33 left in the game, the only puck to get past Evgeni Nabokov came off the right arm of Eric Godard as he went to the San Jose net and had David Hale's rebound bounce off him and into the net at 16:01 of the first period.
It was originally ruled a goal that would have given the Flames a 1-0 lead. However, replays indicated Godard slightly moved his arm towards the puck as he skated towards the net so the goal was waived off.
That would be a critical play in the game as shortly after with Calgary's Matthew Lombardi in the penalty box, San Jose took advantage of the first power-play of the night for either team with Joe Thornton and Roenick combining to set up Clowe with 36 seconds left in the period.
Thornton worked the puck to the front of the net where Roenick made an alert pass to Clowe at the edge of the crease and he fired his third goal of the season past Miikka Kiprusoff.
It was a sweet turn of events for Roenick, who on his previous shift was booed off the ice by the sold-out Pengrowth Saddledome of 19,289. Flames Robyn Regehr had delivered a heavy bodycheck against Roenick at the Flames blue-line that appeared to at least temporarily leave the veteran Shark a bit woozy with him staggering slightly at the blue-line after he got up. He remained there for a couple minutes and was attended to by the San Jose trainer before skating on his own to the bench.
Bernier's goal at 16:22 of the second when he tipped in Craig Rivet's point shot was a significant one in that it marked the first time that Mike Keenan has pulled Kiprusoff replacing him with Curtis McElhinney. Kiprusoff left with 15 saves on 18 shots.
McElhinney faced only two shots in his 23-plus minutes of action giving up Michalek's second goal on San Jose's only shot of the final period.
Notes: Calgary RW Owen Nolan was honoured before the game for appearing in his 1000th NHL game. Among the gifts he received was a Quad ATV from his Flames teammates, a commemorative painting, a silver stick, and a box of wine from his old organization the Sharks. In eight seasons, Nolan played 568 games for the Sharks ranking him third all-time... Injuries to forwards David Moss (concussion) and Wayne Primeau (ankle) Saturday night opened up a spot for LW Eric Nystrom, who was recalled Sunday from Quad City (AHL). It was the third career game for Nystrom, who made his NHL debut back on Oct.10, 2005... San Jose D Kyle McLaren (chest contusion) did not play with Alexei Semenov taking his place and making his San Jose debut.