The Honda rider was in a class of his own on the Spanish track, able to set such a punishing pace at the front that not even championship leader Jorge Lorenzo could live with him.
His winning margin eventually stretched to 6.4s.
Lorenzo did at least have the comfort of finishing second, surrendering just five points in the championship as a result. His lead, boosted by Pedrosa's first lap exit at Misano, now stands at 33 points with just four races to run.
While his championship hopes were not massively dented, on track the damage was more pronounced.
Lorenzo had led the opening five laps, and then tried to stay with Pedrosa once the Honda man made his move. Ultimately he had no answer to his rival's pace however, suffering one massive moment as he tried in vain to pull back an ever-widening gap.
Even as Lorenzo lost ground though he was still faster than the chasing pack, which was led for the majority of the race by Yamaha team-mate Ben Spies.
The American briefly lost out to LCR Honda's Stefan Bradl on lap three, only to see the German fall at Turn 3 half a lap later.
That still left Spies defending from Tech 3 pair Cal Crutchlow and Andrea Dovizioso, with the trio separated by less than one second for much of the race.
Ten laps from the end Dovizioso completed his move from fifth to third, before Crutchlow followed him past Spies one lap later.
Crutchlow remained glued to Dovizioso's wheel for the remainder of the race, attacking several times on the final lap. Dovizioso hung on however to claim his sixth podium of the year for the satellite outfit.
In contrast to that battle, Gresini's Alvaro Bautista was able to take a quiet sixth, his progress aided by a variety of incidents, including that of Bradl.
Ducati's Nicky Hayden also fell early, getting flipped over an advertising boarding as he tried to wrestle his bike from running wide at Turn 16. The heavy impact necessitated a visit to the medical centre, although Hayden was later cleared.
Organisers later added he had been taken to hospital for full checks to rule out any internal injuries.
His Ducati team-mate Valentino Rossi also hit trouble, making contact with Honda's Jonathan Rea - making what could be his last appearance as Casey Stoner's stand-in - on the opening lap.
Rossi dropped out of the top 20 as a result of running massively wide, but fought his way back to eighth, behind Rea.
"It was hard to keep calm throughout the weekend, but it was a good race and I saw immediately I could go faster than (Lorenzo)," Pedrosa said afterwards.
"The bike was working well through the corners and I'm happy to win in front of my fans and family."
"When I was passed (by Pedrosa) I knew I could not keep the pace that I had in the first three laps," Lorenzo admitted.
"So from that point on it was a race for the championship - no mistakes, race for second."