Michalek's second power-play goal of the game, with 3:31 left in the third period, snapped a tie and gave the Sharks a 2-1 win.
From the edge or the crease, Michalek deflected Matt Carle's shot past Khabibulin. The goal gave the Sharks their eighth straight win over the Blackhawks, with seven of the victories in regulation.
The Sharks dominated through most of the game, outshooting the Blackhawks 32-17.
"We talked about having to work hard 60 minutes and that's what we did today," Michalek said. "We had all the chances and finally scored the second goal."
Michalek's goals were his first two of the season. He was hampered in the preseason with an arm injury, but has been in the lineup for all four of San Jose's regular-season contests.
"It's nice I scored today," he said. "It's good for my confidence. I had some chances in our first three games."
Although Khabibulin turned in a strong, 30-save performance, the Sharks' ability to convert two of six power plays finally gave them the win. San Jose goalie Evgeni Nabokov blocked 16 shots.
"We had our chances," San Jose coach Ron Wilson said. "I think tonight was the best game I've ever seen Khabibulin play against us.
"It was getting a little frustrating, but it didn't affect our play," Wilson added. "We have to use our speed and particularly our size. Tonight, the way we were skating and playing, any team will have trouble down low against us."
Chicago rookie Jonathan Toews scored on his first shot in his first NHL game to give the Blackhawks a 1-0 lead at 13:43 in the first period.
"It was a great moment," Toews said, "but the bigger picture is the game tonight and I was disappointed not to come out on top."
After Toews was sent off for a hooking penalty in the second period, Michalek scored his first power-play goal, at the 10:28 mark.
Toews, the Blackhawks top draft pick and third overall in 2006, connected on his sixth shift. The 19-year-old forward had missed Chicago's first two games with a broken right index finger, suffered in a Sept. 19 preseason contest.
Toews centered a line with wingers Tuomo Ruutu and rookie Patrick Kane, the first-overall pick in the 2007 NHL Entry Draft.
Toews took a pass at the San Jose blue line, barreled past Sharks Carle and beat Nabokov high on the glove side from the right circle for the opening goal.
Khabibulin stopped San Jose's Joe Pavelski with a glove save on a short-handed breakaway at 8:30 of the second.
While Toews was serving his second hooking penalty of the game, Michalek tied it 1-all at 10:28 of the second. Michalek fired a shot between Khabibulin's legs from the low edge of the right circle after working a give-and-go with Patrick Marleau.
San Jose's first goal came on its 21st shot.
Chicago killed a double-minor penalty to Brent Seabrook early in the third.
Toews was whistled for his NHL first penalty, for hooking, late in the first period. ... Blackhawks RW Martin Havlat missed his second game because of a right shoulder injury and is out indefinitely. Chicago D Andrei Zyuzin missed his third game because of a groin injury. ... San Jose D Douglas Murray and C Patrick Rissmiller were healthy scratches for the first time this season. Four Sharks sat out with injuries -- D Brad Norton (back), D Alex Semenov (back) C Tomas Pilhal (shoulder) and RW Devin Setoguchi (ankle).
Copyright by STATS LLC and The Associated Press
Arena: United Center Location: Chicago, Illinois
Referees: Chris Lee Linesmen: Andy McElman, Dan Schachte
Attendance: 10,122 (51.3% full)
Team Stat Comparison
Power Play Goals
Power Play Opportunities
Shots on Goal
Jonathan Toews (1)
Assists: Brent Seabrook, Patrick Kane
Milan Michalek (2)
(Power Play) Assists: Patrick Marleau, Craig Rivet
Milan Michalek (2)
(Power Play) Assists: Matt Carle, Craig Rivet