The Spanish rider won his third successive Grand Prix at Sachsenring with Jorge Lorenzo finishing second and Andrea Dovizioso in third spot.
Pedrosa's Honda team-mate Casey Stoner fell while trying to challenge Pedrosa on the final lap, handing Yamaha Jorge Lorenzo second, and with it the championship lead.
Andrea Dovizioso meanwhile captured his third podium for the Tech 3 squad, having withstood heavy pressure first from team-mate Cal Crutchlow and then from Yamaha factory rider Ben Spies.
From as early as the first lap there were signs no one else could match the factory Hondas, and so it proved as Stoner - having picked off Pedrosa though Turns 9/10 on the second lap - and the Spaniard edged away from the field.
Pedrosa at least kept it interesting at the front as the Hondas left the others trailing, refusing to allow Stoner to pull a gap of more than half a second at the front.
Eleven laps from the end Pedrosa picked off Stoner at Turn 1, but the Australian took up the chase and was on Pedrosa's tail on the final lap when he lost the front of his bike and dropped it into the gravel at Turn 12.
Lorenzo was therefore gifted second, and with it a 20-point lead in the championship. He was looking at a four-point deficit just two corners from the finish.
His lonely ride was in stark contrast to the battle happening behind him. Spies initially held fourth, but on lap eight was picked off by Dovizioso at Turn 1 and then Crutchlow at Turn 12.
There was nothing to choose between the Tech 3 men for almost the entire race, while Spies was able to rejoin on the back and make it a three-way fight, the trio rarely separated by less than two tenths of a second.
The scrap came to a premature conclusion however when Crutchlow ran deep and into the gravel at Turn 1 five laps from the end, dropping to 11th. Without his pressure Dovizioso was able to resist Spies, claim third and move ahead of Crutchlow in the championship.
Not to be deprived of action, Crutchlow then got himself involved in a six-way scrap for fifth. LCR Honda's Stefan Bradl held the position, having resisted pressure from a trio of Ducatis.
Crutchlow and Gresini Honda's Alvaro Bautista, who had scythed through the field after his Dutch TT penalty forced him to start from the back of the grid, also got involved in the final two laps.
Although rain was a pervading threat, it only began to arrive on the final lap. The race was therefore almost completely dry and, aside from Stoner, Speed Master Aprilia's Mattia Pasini was the only other crasher, retiring on lap five.