* Vettel wins in Red Bull one-two
* World champion triumphs after ignoring team orders
* Alonso crashes out
* Hamilton third for Mercedes despite pitting at McLaren
* Perez scores his first points for McLaren
By John O'Brien
SEPANG, Malaysia, March 24 (Reuters) - Formula One world champion Sebastian Vettel won a controversial Malaysian Grand Prix on Sunday after defying orders to back off and let Red Bull team mate Mark Webber take the chequered flag ahead of him.
The German's 27th victory, from pole and equalling the tally of triple champion Jackie Stewart in the all-time lists, was full of bad blood on an action-packed afternoon that started with a rainstorm and ended in recrimination and dark scowls on the podium.
"This is not a victory that I'm very proud of because it should have been Mark's," the chastened German, who took the lead after the team had asked both drivers to turn down the engine and look after the tyres, conceded after spraying champagne in muted podium celebrations.
The Mercedes duo of Lewis Hamilton and Nico Rosberg finished third and fourth, crossing the line in close formation 12 seconds behind Vettel after obeying orders from their pitwall to hold station.
Unlike compatriot Vettel, Rosberg did as he was told despite telling the team repeatedly that he was quicker and should be allowed past Hamilton.
"If I'm honest I really feel Nico should be standing here," ssid Hamilton after his first podium with Mercedes since he moved from McLaren. "I can't say it's the best feeling being up here (on the podium) but racing is racing."
Last year's winner Fernando Alonso crashed out on the second lap after he hit the rear of Vettel's Red Bull and damaged his front wing, which broke off and became wedged under the Ferrari's chassis.
Vettel's first win of the season sent him top of the standings with 40 points to Kimi Raikkonen's 31. Webber is third overall on 26. Red Bull took the lead in the constructors' championship from Ferrari after two races.
"The overriding emotion is that we scored 43 points, a maximum score, and a fantastic performance by the team and the car today and against a backdrop of tyres that we didn't think would go more than five or six laps," said Red Bull principal Christian Horner.
"We told the drivers to maintain position to the end of the race, look after the tyres. The biggest fear was running out of tyres. Sebastian took it into his own hands to (overtake)...he wanted to win that race.
"We know there is a bit of history between them...so it's one of those things and the type of thing we will sit down and talk about internally."
The cars started on intermediate tyres following a heavy downpour in the mid-afternoon with Webber taking the lead at the second round of pitstops after starting fifth.
The two Red Bulls fought a thrilling battle with Vettel's frustration becoming increasingly apparent while Webber kept him covered defensively.
"Mark is too slow, get him out of the way," the German told the team over the radio at one point.
"I did a mistake, I'm not proud I did it," Vettel, given the cold shoulder by Webber before they went on the podium, told reporters later.
Webber made his anger evident. "In the end we got the right strategy and after the last stop, the team told me to turn the engine down," said the Australian.
"Seb made his own decisions and will have protection as usual. I turned my engine down and as we know he's a quick pedaller."
Behind them, Hamilton and Rosberg showed Mercedes were a force to reckon with after a solid and consistent performance - even if the Briton found it hard to shrug off old habits by stopping in the McLaren pits.
The gaffe was the comedy moment of a race otherwise short on smiles, with Hamilton waved through by mechanics before locating his own team two garages down.
"Feel free to pop in and say "hi" any time, @LewisHamilton!" McLaren joked on their Twitter feed shortly after.
Ferrari's Felipe Massa came home a distant fifth, after qualifying on the front row. The Lotus pair of Romain Grosjean and Raikkonen, winner in Melbourne a week ago, took the sixth and seventh spots.
Alonso's 200th grand prix was short-lived with Ferrari appearing to make a major error in keeping the Spaniard on track with a broken wing rather than bringing him in to the pits.
The wing broke off on the start-finish straight as Webber passed him for second place and the Ferrari ran off into the gravel with Alonso a helpless passenger.
McLaren's Jenson Button was enjoying a good race and briefly led before a botched stop left him stranded in the pitlane as mechanics raced to tighten a loose wheel. He dropped down to 12th place before retiring on the penultimate lap.
Mexican team mate Sergio Perez took his first points for McLaren, and the first since he was announced last year as Hamilton's replacement, by finishing ninth behind Sauber's Nico Hulkenberg.
French driver Jean-Eric Vergne grabbed the final point for Toro Rosso. (Editing by Patrick Johnston/Alan Baldwin)