A fourth win in the last five races has pulled Pedrosa to within 28 points of the Yamaha rider but with just three races left, the championship is still Lorenzo's to lose.
"We did what we needed to do," Pedrosa told reporters. "It's just a pity that there is no one else who can stay with us because every race I win, (Lorenzo's) been second.
"But anyway, it's a great feeling to win races and we are doing it now."
Alvaro Bautista's third place for Honda made it a Spanish sweep of the podium on an overcast day at Motegi's Twin Ring circuit.
Lorenzo, world champion in 2010, again failed to capitalise on his sixth pole of the season, leading in the early stages but never able to pull away from a dogged Pedrosa.
It was the fifth time in succession that Lorenzo has failed to turn pole position into victory, the only time he went on to win the race was at the 2012 season-opener in Qatar.
"I was completely at the maximum trying to stay with Dani, but today it was maybe too much difference, the performance on the straights," said Lorenzo.
"I tried to stay with him but it was impossible, maybe next time. For sure the Championship is closer now, but we are still very competitive and have the chance to win."
Pedrosa pounced 13 laps from the finish and stretched his advantage at the front to over a second within two laps of overtaking Lorenzo.
Pedrosa, who has now claimed a career-best five wins in a MotoGP season, won in a time of 42 minutes, 31.569 seconds.
Not wishing to take any risks given his comfortable lead in the standings, Lorenzo eased off the throttle to coast home in a time of 42:35.844.
Lorenzo has 310 points to Pedrosa's 282 in the championship standings, with world champion Casey Stoner on 197.
Bautista's third place came after a hair-raising fight with Briton Cal Crutchlow, whose Yamaha ran out of fuel on the final lap to end the battle on a rather anti-climactic note.
Australian Stoner finished a creditable fifth in his return after ankle surgery, although clearly not fully fit and still in some pain he struggled as the race wore on.
Seven-times premier class champion Valentino Rossi finished a dejected-looking seventh for Ducati.
Spaniard Marc Marquez tore through the field to claim his eighth victory of the Moto2 season, giving him the opportunity to clinch the title in Malaysia next week.
The Suter rider's win, in 42:56.171, was all the more remarkable after stalling on the start line and getting away virtually last in the 32-bike field.
Britain's Danny Kent claimed his maiden grand prix win in a wild finish to the Moto3 race.
German Sandro Cortese was on course to claim the title on the last lap, but his KTM machine crashed out after he clashed with Alessandro Tonucci, gifting team mate Kent victory.