Marquez grazed the back of Pedrosa’s bike when he was trying to pass him with 18 laps to go, causing Pedrosa to lose control and slide down the track with sparks flying.
“I touched him a little with the front of my bike, and they tell me I may have broken a cable and that’s why he fell,” said Marquez. “It was very unlucky. That doesn’t usually happen.”
The 20-year-old Marquez went on to overtake defending champion Jorge Lorenzo, who had jumped ahead with a great start on his Yamaha.
Marquez finished the race at the 5-kilometer (3.15-miles) MotorLand Aragon circuit in 42 minutes, 3.4 seconds. Lorenzo was 1.3 seconds behind.
“We knew before the race that it was going to be tough,” said Lorenzo. “We had a lot of difficulties this weekend. The bike was unstable. But there are no excuses. Marc was faster and he deserved to win.”
Valentino Rossi finished third, more than 12 seconds back on his Yamaha, ending a run of four straight fourth-place finishes.
Marquez’s sixth win of the season gave him one more than Lorenzo and broke his closest challenger’s run of winning the previous two races.
Marquez is aiming to become the first rookie to win the championship since American Kenny Roberts in 1978.
Marquez leads Lorenzo by 39 points with four races left. Pedrosa came in level on points with Lorenzo in second place but now trails Marquez by 59.
Pedrosa, who won here last year and turned 28 on Sunday, had to be carried off the track by the medical crew. He later said that he was fine except for some pain in his pelvis.
Pedrosa, however, was angry at both his teammate’s riding style and the race stewards’ decision not to penalize the incident and others like it.
“It’s easy to sum up what happened. Marc always rides to the limit when he has riders in front,” said Pedrosa. “He hit me from behind and that’s where my race ended. It doesn’t matter what he says.
“I would also like to say something about the race stewards. There have been some things that have happened in recent years. We pilots with more experience have tried to calm down those with less, but (the stewards) have just let things go by as if nothing happened.”
Spanish riders swept the two lesser categories.
In Moto2, Nicolas Terol secured his second win of the season after starting on pole. Esteve Rabat finished second, followed by Pol Espargaro in third.
Britain’s Scott Redding, who had surgery on his right arm to treat a loss of strength on Thursday, finished fourth and maintained his lead. Redding has 202 points. Espargaro is next with 179.
In Moto3, Alex Rins got his fifth victory of the season by pulling away down the final stretch when Maverick Vinales had a problem shifting gears.
Vinales finished second, ahead of Alex Marquez and leader Luis Salom in fourth.
Salom has 259 points. Rins is second with 250, followed by Vinales with 247.