Dani Pedrosa celebrates on the podium after winning the Malaysian Grand Prix MotoGP motorcycling race on Sunday. Photo: AFP

MotoGP championship leader Valentino Rossi will start the season finale in Valencia from the back of the grid after the Italian was penalized for clashing with Marc Marquez at the Malaysian Grand Prix on Sunday.

Dani Pedrosa claimed victory at ­Sepang and was followed home by Rossi's championship rival and ­Yamaha teammate Jorge Lorenzo, who has now closed the gap to seven points ahead of the decider in Spain in two weeks' time.

Rossi finished third but had an ­anxious wait to see if he would keep the points after making contact with Marquez and sending the Spaniard spinning into the gravel.

After an inquiry, Race Direction opted against docking the seven-time premier class champion any points but imposed a "three-point penalty" that will see him start at the back of the field in Valencia.

The Yamaha team have appealed the decision.

Prior to the race, Rossi had claimed former champion Marquez wanted fellow Spaniard Lorenzo to win the championship instead of him and the simmering relationship between the pair boiled over at the Sepang International Circuit.

The duo darted into corners trying to get the upper hand, swapping ­places and touching wheels a number of times until Rossi slowed at Turn 14, forced Marquez wide and then flicked out a knee, which resulted in his rival's Honda sliding into the gravel.

Rossi said it was a racing incident and regretted his rival had crashed out.

By avoiding disqualification, Rossi remains on 312 points ahead of the Valencia Grand Prix, seven ahead of Lorenzo with 25 available for victory in Spain.

There was more drama on the podium as the pro-Rossi Malaysian crowd booed Lorenzo when he picked up his second-place prize, with the Spaniard storming off immediately after the anthems and not waiting to pose for photographs.

Rossi then declined to attend the traditional post-race news conference where double world champion ­Lorenzo said, "Valentino should have the same points as Marc, Marc would have been third or fourth."

"Valentino should be here to explain it," said Pedrosa, whose brilliant ride from pole to flag was almost forgotten amid the drama.