Stoner, who started from pole, was taken out of the race by Rossi who slid into him during an ambitious overtaking move.
Rossi apologised to Stoner for the incident which ruined the Australian’s chances of opening up a good lead in the championship.
After winning the season-opening Qatar GP last month for Honda, Stoner led Sunday’s race with 20 laps to go when he and Rossi clashed and crashed to the track.
While world champion Jorge Lorenzo went on to take the race from fellow Spaniard Dani Pedrosa, Stoner was unable to continue.
Rossi, who eventually finished fifth, immediately entered the Honda garage at the end of the race to apologise to Stoner.
“You had something with your shoulder did you?” Stoner said to the Italian, smiling.
“Obviously your ambition outweighs your talent.”
“With the accident, I heard Valentino arriving and I wasn’t worried about anyone passing me at that point in the race so I gave him plenty of room,” Stoner said.
“It was a racing incident and there’s not much we can do.
“What is more frustrating is the reaction of the stewards and their assistance for Valentino and not for me – it was unbelievable.”
Rossi told Italia1 television: “It’s completely my mistake and I have to say sorry to Casey.
“I know that he’s very angry because he didn’t make any mistakes. I went straight to say sorry.”
Lorenzo was a much happier figure than Stoner.
“It was a hard race but I am happy with the win,” Lorenzo said. “We had some luck, without the fall of Stoner we would not have won.”