It was a good day for Red Bull as Mark Webber finished second behind teammate Vettel.
Reigning world champion Sebastian Vettel took the advantage in Malaysia as his closest competitors failed to impress.
The German won a controversial race which saw him and teammate Mark Webber fall out over podium positions.
Tension was clear between the two drivers as Vettel was reprimanded by his team for overtaking the Australian.
“I messed up today,” the current world champion said on the BBC.
“I owe an explanation to Mark and the team and that’s it. For sure it’s not a victory I’m very proud of because it should have been Mark’s.”
Mercedes’ Lewis Hamilton finished third despite having a brief memory lapse and trying to pit with his old team McLaren.
Fernando Alonso retired in just the second lap after damaging his front wing when he hit Vettel in the first.
Last week’s winner in Australia, Kimi Raikkonen, finished seventh for Lotus whilst Alonso’s teammate Felipe Massa battled to fifth.
There were several calamities in the pits as Jenson Button was forced to end his race two laps from the end when his front wheel was not attached properly.
Force India had a nightmare as they struggled on two occasions to attach wheel nuts to their cars and in the end both drivers retired from the race.
Victory for Vettel puts him on 40 points for the 2013 season, nine points ahead of second-placed Raikkonen.
Webber is third in the drivers’ championship on 26 points, just in front of Hamilton (25) and Massa (22).
It continues to be a poor season for McLaren meanwhile as neither of their drivers make the top eight drivers currently, although Sergio Perez was among the points in Malaysia finishing ninth.
There is a three week break now until the next Grand Prix in China, giving time for Vettel and Webber to try and settle their differences.