SEPANG, Malaysia -- Sebastian Vettel's 27th victory in Formula One didn't earn him a lot of admiration. He even had to apologize for it.

The three-time defending champion ignored team orders Sunday and overtook fellow Red Bull driver Mark Webber toward the end to win the Malaysian Grand Prix, having been told to stand down and cruise to a 1-2 finish.

The German's move left Webber fuming and had team officials remonstrating Vettel publicly after the race. Vettel apologized, but said he didn't realize he had been told to hold back.

"Mark should have won," said Vettel, who now leads the championship standings by nine points ahead of Lotus driver Kimi Raikkonen. "I made a big mistake today and we should have stayed in the position. I messed up in that situation and took the lead from Mark and can see now he is upset. Apologies to Mark. The result is there and all I can say is that I didn't do it deliberately."

Webber refused to acknowledge his teammate after the race, and said he had been told by the team to keep a slower pace to save the tires to the end.

"Seb made his own decisions and he will have protection as usual and that's the way it goes," Webber said. "It's still very raw at the moment."

Asked if the fight had him reconsidering his role at Red Bull, Webber said he had "a lot of things going through my mind."

Vettel's decision to ignore team orders was made extra glaring by the fight for third place between Mercedes drivers Lewis Hamilton and Nico Rosberg. In a similar situation, Rosberg was told repeatedly not to pass Hamilton, and obeyed -- giving the Briton his first podium finish with his new team.

"I don't feel spectacular sitting here. Nico deserved to be where I am right now," Hamilton said. "Obviously, the team thought for position in the championship it was logical to stay in the position we are in. I say congratulations to Nico. He drove a much smarter and controlled race than I did."

Vettel started from pole but Webber grabbed the lead on the ninth lap and stayed in front for much of the race. Vettel had complained over the team radio earlier that "Mark is too slow" and that they should let him pass. The team response was for the German to be "patient."

He clearly ran out of patience on the 46th lap, making an aggressive move with the cars almost touching as the German grabbed the lead -- with team officials immediately calling him "silly" over the radio.

Team principal Christian Horner said Vettel's decision made for a "hugely uncomfortable" situation within the team.

"It's frustrating. Formula One is both a team and an individual sport and sometimes there is a conflict between a driver's desire and a team's interest," Horner said. "What happened today is something that shouldn't have happened. It's something that Sebastian has apologized for and it's something that we will discuss internally as a team."

The incident brought back memories of the 2010 Turkish Grand Prix, when Webber was also leading ahead of Vettel. That time, the two cars crashed when Vettel tried to overtake, spoiling what was a near-certain 1-2 finish.

"Let's be honest here. There has never been a great deal of trust between the two of them since Turkey in (2010) but there is a respect," Horner said. "If you think of Brazil (in 2012), Mark was told to hold his position and started racing him. They are race drivers and they will push to the limit. That is part of what their DNA is that is part of why we signed them to do the job, and why they performed so well for us as a pairing over the past five years."

Mercedes team principal Ross Brawn had more success with his orders, after imploring Rosberg to back off from Hamilton who was struggling to make his fuel last. Brawn told Rosberg that "I want to bring these cars home," and the German complied. As Brawn congratulated him over the radio, Rosberg told him to "remember this one.'

Rosberg called it a "great day" for the team but acknowledged that the finish was not ideal.

"Of course, it was disappointing for me having to hold position but I understand the team's decision to safeguard our positions and to make sure that both cars got to the end with a strong team finish, especially in light of the tough times behind us," he said.

Hamilton earlier endured an embarrassing moment when he drove into his former team McLaren's pits before correcting himself and heading to Mercedes, which he joined ahead of this season.

The finish to the race could also cause grumblings from fans, who prefer to see the drivers duel it out for the win rather than having team orders decide the result.

"You know, it's not perfect," Toto Wolff, the Mercedes team executive director, said. "From the sporting point of view, it's not what people want to see, nor what I want to see. But sometimes you have to make a call and you have to make decision and Ross did that to bring home third and fourth."

It was a disastrous day for Ferrari's Fernando Alonso, who crashed out of the race on the second lap after damaging his front wing when he bumped Vettel a lap earlier. His teammate Felipe Massa started poorly but managed to finish fifth.

"Bad luck today, as always over 19 races will be compensated and we are ready to recover good points in the next race," Alonso tweeted.

McLaren's troubles also continued, as a botched pit stop dropped 2009 champion Jenson Button to 14th. The Briton then retired with two laps remaining while his teammate, Sergio Perez, finished ninth.