McLaren's Hamilton retired with a suspected gearbox failure, only his second failure to score this season, and dropped to second place overall and four points adrift.
Vettel, starting on pole position for the seventh time in 12 races but again failing to convert the advantage, fell foul of the safety car rules and finished third behind Ferrari's Fernando Alonso.
Webber now has 161 points to Hamilton's 157, with Vettel on 151 and McLaren's Jenson Button on 147. In one of the closest battles in years, Alonso has 141.