On lap 46 team boss Christian Horner was heard to tell the triple world champion that his dogged attacks against his team-mate were getting "silly" - just as the German finally made the most of his DRS advantage and made a move stick. A disgruntled Webber hung on for second.
After the race Vettel was told by his team that "there will be some explaining to do" while the broadcasters blocked Webber's response when congratulated on his second place finish by his pit crew.
Post-race Webber added: "I want to race as well, but in the end the team made a decision which we always say before the start of the race is how it's probably going to be: we look after the tyres and get the cars to the end. In the end Seb made his own decisions today and will have protection as usual, and that's the way it goes."
Vettel later apologised in an official team statement: "I took quite a lot of risk to pass him and I should have behaved better. It doesn't help his feelings right now. Apologies to Mark and now result is there, but all I can say is that I didn't do it deliberately."
Meanwhile, as Hamilton slipped off the pace of the lead duo he found himself under attack from his team-mate, Nico Rosberg, who was consistently quick, if less dramatic, throughout the entire race. The race between the team-mates raged for many laps, until team boss Ross Brawn ordered an end to the battle with a couple of laps to run, leaving Hamilton to take the final podium spot.
Following the race, Rosberg appeared to suggest he could have beaten Hamilton, asking the team to "remember this one" on the radio.
Ferrari's Felipe Massa enjoyed a competitive but relatively quiet run to fifth. Team-mate Fernando Alonso had enjoyed a great start to the race, but slid in to the back of Vettel's Red Bull early in the opening lap, damaging his front wing. At the start of the second lap the front wing broke, pitching him off the track and in to retirement.
Jenson Button also showed decent pace, but his hopes of a points finish were ruined when his McLaren team failed to fit a wheel correctly at one of his tyre stops. The stricken car was recovered in the pitlane and the errant tyre fixed, with Button going on to show good pace before retiring when it became clear he wouldn't score points.
2013 Malaysian Grand Prix top ten results - all timing unofficial 1. Vettel (Red Bull-Renault); 2. Webber (Red Bull-Renault) +4.298sec; 3. Hamilton (Mercedes) +12.1sec; 4. Rosberg (Mercedes) +12.6sec; 5. Massa (Ferrari) + 25.6sec; 6. Grosjean (Lotus-Renault) +35.5sec; 7. Raikkonen (Lotus-Renault) +48.4sec; 8. Hulkenberg (Sauber-Ferrari) +53.0sec; 9. Perez (McLaren-Mercedes) +72.3sec; 10. Vergne (Toro Rosso-Ferrari) +87.1sec.
F1 drivers championship points: 1. Vettel 40; 2. Raikkonen 31; 3. Webber 26; 4. Hamilton 25; 5. Massa 22; 6. Alonso 18; 7. Rosberg 12; 8. Grosjean 9; 9. Sutil 6; 10. Di Resta 4; 11. Hulkenberg 4; 12. Button 2; 13. Perez 2; 14. Vergne 1.
F1 manufacturers championship points: 1. Red Bull-Renault 66; 2. Lotus-Renault 40; 3. Ferrari 40; 4. Mercedes 37; 5 Force India-Mercedes 10; 6. McLaren-Mercedes 4; 7. Sauber-Ferrari 4; 8. Toro Rosso-Ferrari 1.