Peter Sauber, the Sauber team chief, has refuted claims a conspiracy was at the heart of yesterday's Malaysian Grand Prix.

The Swiss team missed out on a historic win by just 2.263 seconds as rising Mexican star Sergio Perez pushed Ferrari's Fernando Alonso to the line at the Sepang International Circuit. At one stage on lap 40 Perez had closed to within 1.3sec, only for the team to not follow Ferrari's lead and bring him in when the conditions demanded a change from intermediate to dry tyres.

Then on lap 50 Perez made an error of his own when he ran wide at turn 14 when he was poised to pass Alonso after again cutting the gap to 0.5sec.

The theory was, as Sauber are powered by Ferrari engines and Perez remains a product of the Maranello marque's young driver academy, that the 22-year-old was called to file in behind Alonso.Fuel has been added to the fire by the fact Perez's engineer was heard over the team radio telling him "we need the position".

"He meant that we needed the result. It's a misunderstanding," said Sauber, when asked about the message. "It was because that behind us, all the midfield teams, our main competitors, scored points.

"So it was important we kept the result and not the position."

Pressed on whether Perez had been told to stay behind Alonso, Sauber said: "No. We told him 'be careful we need the result'."

Sauber was then quizzed on whether there had been any discussion with Ferrari, but he said: "No. 100% no. 100% nothing. We had no discussion about Checo (Perez) nor the position."

It took the gloss off what was a stunning drive from Perez as he achieved his finest result in Formula One and Sauber's highest position since the 2008 Belgian Grand Prix when Nick Heidfeld was runner -up, and at a time when the team were heavily backed by BMW.

Perez proved himself in very tough conditions as the race was suspended for 51 minutes after nine laps due to heavy rain. In high humidity the track did not start to dry out until near the end, yet Perez managed to reel in Alonso on inters and dry tyres, only to fall short.

"I think I could have won it, definitely," said Perez, who realised the race was an opportunity missed to record his first victory in F1.

"I was catching Fernando toward the end of the race, but I ran wide enough to go on to the wet and I just lost control of the car, went straight and lost the fight for the victory.

"In the end, second is a great result for the team. Many points."

Perez has now scored more points than he managed in his rookie year last season, and the team have 30 overall, just 14 behind their total achievement in 2011.

For Ferrari, the result will lift them out of the doldrums, yet Alonso maintains the win "changes nothing" given the relative uncompetitiveness of their car.

"The win is a big surprise because we were not competitive in Australia, nor here," said the Spaniard.

"We are in a position we don't want, fighting to get into Q3 and then fighting to score some points.

"We want to fight for poles, victories, because after the first two races of the championship we find ourselves off the pace."

Lewis Hamilton had to again settle for third from pole and trails Alonso in the championship by five points.

On this occasion, after being far from happy with third a week ago in his McLaren, the tune had changed. "We can be satisfied," said the Englishman.

"We would have liked more points, but I guess I can't complain. I'm on the podium for a second week in-a-row so I'm pretty happy."

Team-mate Jenson Button, who was triumphant in Australia a week ago, finished 14th after a collision with HRT's Narain Karthikeyan forced a front-wing change shortly after the restart.

Reigning champion Sebastian Vettel also missed out on points as he was 11th after his own clash with Karthikeyan late on that led to a left-rear puncture.

Other notable achievements were Bruno Senna, who finished a career-high sixth, giving Williams eight points, three more than they scored in the whole of last season, while Scotland's Paul di Resta took seventh for Force India.