Webber finished 10th but video evidence showed he had gained an advantage late in the race for leaving the track, leading to a 20-second time penalty as the race had finished when his transgression was spotted.
Sauber's Sergio Perez originally finished 11th but leapfrogged Webber in the standings to pick up one point.
Following the deduction, the Australian remains in fifth place in the drivers' championship on 132 points with six rounds remaining, 62 behind leader Fernando Alonso. Perez stays in ninth place on 66.
Webber's Red Bull team mate Sebastian Vettel won the race around the floodlit Marina Bay Street Circuit to close within 29 points of Alonso.