Kovalainen, 26, won from Toyota's Timo Glock with Ferrari's Kimi Raikkonen in third place.
Brazilian novice Lucas di Grassi was unveiled on Tuesday as ex-Toyota driver Timo Glock's team-mate.
However, he passed the slowing Toyota of Timo Glock accelerating out of the final corner to create F1 history.
But compatriot and Virgin driver Timo Glock believes Schumacher's return is a certainty.
BBC: Mercedes boss hints at F1 return for Michael Schumacher
Meanwhile, Russian team Marussia has replaced Timo Glock with Brazil's Luis Razia as its second driver for the 2013 season.
Toyota's Timo Glock secured his highest placing this season coming in second with Renault's Fernando Alonso coming home in third.
Toyota driver Timo Glock was fourth with Toro Rosso's Sebastian Vettel following up his win in Italy this month with fifth.
But at the moment we have Brazilian driver Lucas di Grassi and German driver Timo Glock, and we're perfectly happy with that.
BBC: Russian supercar firm Marussia takes over Virgin Racing
The Toyota of Timo Glock was fourth, ahead of Ferrari's Felipe Massa.
For rookie driver Timo Glock it was all about the anticipation.
One of those struggling outfits, Virgin Racing, suffered badly from technical problems as a gearbox leakage and telemetry problems blighted Lucas di Grassi and Timo Glock's second sessions.
BBC: Lewis Hamilton fastest in Friday Australian GP practice
In addition to Campos signing Senna, Lotus have signed experienced race-winners Jarno Trulli and Heikki Kovalainen while Timo Glock and Lucas di Grassi will drive for Virgin Racing.
Toyota's Kamui Kobayashi, who is deputising for the injured Timo Glock, was fifth, followed by Toro Rosso's Sebastien Buemi and Red Bull's Mark Webber, winner in Brazil last time out.
McLaren's Heikki Kovalainen, who had finished second to Hamilton earlier in the day, was fourth in the afternoon, followed by the BMW Sauber of Robert Kubica and Toyota's Timo Glock.
Williams, who had high hopes for Malaysia after Nico Rosberg finished third in Melbourne, suffered when he collided with Toyota's Timo Glock and Kazuki Nakajima punctured a tire.
Forced to go to the pits to change tires, Hamilton was passed by Sebastien Vettel and Timo Glock -- leaving him in sixth position and potentially costing him the world title.
The 25-year-old German Timo Glock completes the driving team.
Toyota, third in the constructors' championship after strong performances in this season's first five races, failed to shine as Timo Glock and Jarno Trulli could not finish among the 10 quickest times.
Hamilton clinched the title when he passed Timo Glock accelerating out of the final corner of the race to snatch the drivers' crown from Felipe Massa, who took the chequered flag ahead of him.
There was still time for a late flurry as Toyota's Japanese rookie driver Kamui Kobayashi, who is once again deputising for the injured Timo Glock, moved up to third position before finishing fifth fastest.
But the McLaren man came good in the end, overtaking Toyota's Timo Glock, who had stayed out on dry tires as the heavens opened, to snatch fifth with the checkered flag in sight.
Nick Heidfeld of BMW took fifth after McLaren's Heikki Kovalainen suffered a puncture with 20 laps to go, with Toyota's Timo Glock and Renault's Nelson Piquet taking the final points positions in seventh and eighth.
Kubica lost a lot of time behind Timo Glock's Toyota between laps 38 and 42, but he was more than able to pull out the advantage he needed in the seven laps before his final stop.
Virgin technical director Nick Wirth is hopeful that Timo Glock will take up the year remaining on his contract and stay with the rookie team in 2011 despite rumours that Renault are interested in the German.
Timo Glock signed a two-year contract with Virgin in 2009 but the German has been linked to other teams, including Renault, while Brazilian Lucas di Grassi's future with Virgin remains uncertain after he lost his main sponsor mid-season.
BBC: Russian supercar firm Marussia takes over Virgin Racing
He won the season-ending Brazilian Grand Prix and began celebrating, but was denied the championship by one point as McLaren's British driver Lewis Hamilton overtook Timo Glock on the final corner to finish fifth and steal the glory.
The top 10 was rounded out by the Toyotas of Timo Glock and Jarno Trulli in sixth and seventh, Fernando Alonso eighth for Renault, with Nico Rosberg ninth in his Williams and Robert Kubica 10th for BMW Sauber.
Hamilton, whose new car is unveiled on Friday, clinched the title in dramatic style on the last corner of the final race in Brazil - passing Toyota's Timo Glock to move into the fifth position he needed to clinch the championship.
At the title-deciding 2008 Brazilian Grand Prix it looked as though he had won the championship only for McLaren's Lewis Hamilton to pass a struggling Timo Glock on the last corner of the last lap and grab the four points he needed to take the crown.
应用推荐