At 15 Khabibulin was included on the Sverdlovsk's Automobilist team. He spent most of his time on the bench, but when he was 17, CSKA Moscow invited him to play for them. In his first season with CSKA, head coach Victor Tikhonov did not let him play as first goaltender, but at the World Junior Championship, Khabibulin was the Soviets' first goalie. Tikhonov took him as third goalie to the 1992 Olympics in Albertville, France, where Khabibulin did not get a chance to play and contribute to the CIS victory.
A talent for goaltending is uncommon, and to be successful in the NHL, a goalie needs outstanding skills and a lot of luck. Khabibulin has both. In 1994, after three seasons with CSKA, he joined the Winnipeg Jets, who had drafted him in the eighth round two years earlier. A lockout at the time prevented the young goalie from playing, but he had a two-way contract, giving him the opportunity to work on his technique in Springfield with the Jets' AHL affiliate. When the short 1994-95 season began, the Russian goalie was doing as well as the Jets' main goaltender, Tim Cheveldae.
At the beginning of the next season, Jets coaches told Khabibulin there would be no distinction between primary and secondary goaltenders, either would be allowed to defend the net equally until the first major error. Cheveldae's performance was uneven, but Khabibulin did not make an error in 15 consecutive games. Then he sustained a knee injury and was forced to leave the ice. Without him, the Jets gained only 13 points in 20 games. When he returned, Khabibulin was able to regain his position as the number one goalie and did not yield it.
In his third season in the NHL, Khabibulin's team moved from Winnipeg to Arizona and was given a new name, the Phoenix Coyotes. In Phoenix, Khabibulin continued to be the leading goalie. By mid season he was in excellent form, with seven shutouts in 27 games. He did not allow a single goal in three consecutive games against the Florida Panthers, the Tampa Bay Lightning and the Chicago Blackhawks. The next two seasons were equally successful for Khabibulin. He set a team record with a total of 126 wins.
In the 1999-00 season the impressive pace of Khabibulin's career slowed down. His strike over a contract dispute proved to be a serious setback. He signed a contract with the IHL's Long Beach Ice Dogs. His outstanding performance led to the hope that before the trade deadline an NHL club would agree to a trade from Phoenix.
On March 5, 2001, after spending the entire 1999-00 season in the IHL, the Coyotes finally traded Khabibulin to the Tampa Bay Lightning in exchange for Mike Johnson, Paul Mara, Ruslan Zainullin and NY Islanders' 2nd round choice (previously acquired, Phoenix selected Matthew Spiller). Khabibulin went on to play two games with the Lightning in 2000-01 before playing his first full season with the team in 2001-02.
Khabibulin played 70 games in his first full season with Tampa Bay and finished with seven shutouts while also leading Team Russia to a bronze medal at the 2002 Winter Olympic Games in Salt Lake City and was named Top Goaltender of the tournament by the IIHF.
Khabibulin and the Lightning continued to improve in 2002-03, clinching their first playoff appearance since 1996 and one year later went on to capture their first Stanley Cup title with a hard-fought seven game series win over the upstart Calgary Flames. Khabibulin recorded 5 shutouts in 23 playoff games, including 3 shutouts in the first-round match-up against the New York Islanders (tied for an NHL record for most shutouts in a playoff round).
During the 2004-05 NHL lockout, Khabibulin was one of many Russian players to return to his homeland, joining the famed Ak Bars Kazan.
In the summer of 2005, Khabibulin signed a deal with the Chicago Blackhawks that made him the highest paid goaltender in the NHL, but Khabibulin was never able to regain his Stanley Cup form in the "Windy City" and following a difficult 2007-08 season, the Blackhawks signed free agent goaltender, Cristobal Huet.
Khabibulin's time in Chicago appeared to be over, he was put on waivers prior to the 2008-09 season, but went unclaimed and speculation was that Khabibulin would soon be traded. However, something unforeseen happened. Khabibulin's play improved dramatically, as did the play of the team in front of him and by the time the 2009 Stanley Cup Playoffs had begun, Khabibulin had re-established himself as the team's number one goaltender.
The Blackhawks went on to eliminate the Calgary Flames and Vancouver Canucks before eventually be ousted by the defending cup champion, Detroit Red Wings.
In the summer of 2009, Khabibulin's roller coaster ride in Chicago would finally come to an end when, as an unrestricted free agent, he signed with the Edmonton Oilers.