The Italian set a quickest lap of one minute 47.001sec in front of defending world champion Valentino Rossi's Yamaha and Ducati's Casey Stoner at Motegi.
"I'm so happy and surprised," Dovizioso told reporters. "We've improved a lot. Normally my style is not to go too fast in practice. I'm sure we can have a strong race." Lorenzo, virtually assured the title after fellow Spaniard Dani Pedrosa fractured his collarbone in Friday's practice, was upset at missing the front row for the first time this year.
"I would have liked to have been on the front row in Japan — Yamaha's home," said Lorenzo after signing a new two-year deal for the team earlier in the day.
"But it's only qualifying and the most important thing is that we're ready for the race. We have a good pace and we only have one or two more small things still to work on.
"This afternoon I tried the new engine for the first time and it felt good in the high gears." Pedrosa, who trails Lorenzo by 56 points with five races remaining, suffered a multiple fracture of his left collarbone on Friday and is likely to miss the next three races.
The Honda rider was the only man in a position to overtake Lorenzo in the world championship.
