(CNN) -- Championship leader Dani Pedrosa claimed his first pole position this season after stunning MotoGP titleholder Jorge Lorenzo with a scorching late lap at Mugello.
The Honda rider will head the starting grid for Sunday's Italian Grand Prix, having relegated his fellow Spaniard Lorenzo to second for Yamaha.
Andrea Dovizioso secured the final place on the front row for home team Ducati, despite angering Pedrosa with his tactics in Saturday's qualifying and receiving a shake of the fist during the session.
"He was trying to follow me," Pedrosa told the MotoGP website after clocking one minute 47.157 seconds to clinch the 25 pole of his career. "I understand his position. It was not only him, he was just one of them, but everything is alright.
"It was a hard session at the end. I could not really find a space to do a lap time -- many riders were behind me. I was not high up in the order before my last lap, but was able to do a great lap."
Lorenzo, who trails Pedrosa by 17 points in third overall, had been seeking his third pole in five attempts this year.
However, motorcycling's two-time world champion missed out by 0.069 seconds despite beating Pedrosa's record lap time from last year.
"I was surprised by my lap time, that was really impressive and I didn't expect it," said the Mallorcan, who won last year's race from Pedrosa. "I also didn't expect the lap time from Dani on the second try. I expected to be on pole, but that happens sometimes...
"We have to try to make a good start to lead the race at the beginning because we have strong pace on the first two laps. It is going to be really difficult, as Dani and his team have improved the bike so much and he has improved his riding style."
Dovizioso, who injured his neck after crashing on Friday, sympathized with Pedrosa but said he had done nothing wrong to his former teammate.
"He complained because too many riders delayed him, but I can understand him because he was fast and wanted a clear track to try and do the best," the 27-year-old Italian said.
"But when you haven't disrupted his fast lap, he can't say anything."
Britain's Cal Crutchlow heads the second row in fourth for Monster Yamaha Tech 3, ahead of Germany's Stefan Bradl on a Honda LCR.
Pedrosa's new Honda Repsol teammate Marc Marquez will start back in sixth after three crashes in the past two days meant he did not qualify in the top-10 and had to go through the eliminator for the first time in his rookie season.
The 20-year-old is the only rider to have finished on the podium in all four races, and trails Pedrosa by six points in the standings.
"Sixth place today was the best that we could have hoped for and I am very happy with this result," he says, having missed out on the front row while equaling his grid position of the season-opening Qatar Grand Prix.
"At the end of qualifying I was able to put in a hot lap, but the race tomorrow is going to be difficult and tough. I won't be 100% physically because I'm bruised and sore; my shoulder is bothering me the most and we will see how it responds tomorrow."
Marquez will start one place ahead of seven-time world champion Valentino Rossi, who had been third for Yamaha until he was bumped down the times late on.
"Unfortunately I have to start on the third row but I'm quite happy because my pace is quite good, so I think with a good start I can do a good race," said the Italian, who won seven times at Mugello between 2002-2008.
American Nicky Hayden was eighth fastest on the second Ducati, with Spain's Alvaro Bautista rounding out the third row.