Valentino Rossi of Movistar Yamaha MotoGP. Photo: KIMIMASA MAYAMA

Nine-time world champion Valentino Rossi stormed to pole position for Sunday's Grand Prix of Japan after clocking the fastest time in qualifying, resuming his campaign to overtake championship leader Marc Marquez.

The Yamaha man timed 1min 43.954sec at the Twin Ring Motegi circuit Saturday to grab his third pole of the season, as he attempts to close a 52-point gap against Honda's Marquez, who will start from second on the grid after finishing 0.180sec behind the Italian, his closest championship rival.

Defending world champion Jorge Lorenzo overcame a spectacular crash earlier in the day and earned the third fastest lap in qualifying to claim a spot on the front row, clocking 0.267sec after his Yamaha teammate.

The second row will be occupied by Ducati's Andrea Dovizioso, LCR Honda's Cal Crutchlow and Suzuki's Aleix Espargaro.

Rossi said his team had struggled to find the right balance for their machine, while he himself felt weak.

"Before (the Saturday afternoon practice) we did a great job as a team, we found a good balance. It will be important to start from pole," he said.

"I am not at 100 percent. I am quite sick and have difficulty breathing," Rossi said. "Race here is always very long and very demanding."

His Yamaha teammate Lorenzo was also content with his performance after being launched from his bike in the morning. He was airlifted to a hospital to check for head trauma but was quickly declared fit for the race.

He was not able to stand up immediately after the crash, with his left leg in particular pain.

After the incident, helped by painkillers and adrenaline, Lorenzo said his bike started to feel better and his lap times began to improve.

"Honestly, I was scared," Lorenzo said of the crash. "All of my body was hurting.

"I am happy with the front row. We have a good potential to fight for a victory tomorrow," Lorenzo said.

His crash came a day after a nasty fall during Friday's practice by Dani Pedrosa, who broke his collarbone and flew back to Spain for an operation.

Marquez said he was gathering momentum on the circuit where he has never won in the premier race category.

The two-time world champion noted Yamaha have traditionally done well on the Honda circuit, known for its stop-and-go layout with a lot of hard braking and acceleration points.

"We are there. We are very close. We are very consistent with our lap time," Marquez said. "We are in the front row. That was our main target."