Triple world champion Marc Marquez was third for Honda.
Rossi has now been a winner across all classes for longer than any other rider in the history of motorcycling, Sunday's victory coming 20 years and 313 days since his first in what was then the 125cc category.
Fellow Italian Andrea Dovizioso finished fifth for Ducati to take over at the top of the standings, four points clear of Yamaha's Spaniard Maverick Vinales who crashed out after starting in 11th place.
Rossi is now third overall and seven points off the lead.
He now has 115 grand prix wins across all classes, second only to compatriot Giacomo Agostini's 122 victories between 1964 and 1977.
"This place is always special," said Rossi of a circuit known as the 'Cathedral' of motorcycling. "I am so happy for me and my team because I'm back in first place after one year and it was a great race."
The victory was Rossi's 10th at Assen but first since the Catalan Grand Prix in Barcelona on June 5 last year.
The Italian took the lead with 15 laps to go after starting fourth, with French Yamaha Tech3 rider Johann Zarco on pole for the first time, but was then overtaken by Petrucci with five remaining after rain began to fall.
Rossi hit back on the following lap and held on to the finish.
Zarco fell out of contention after pitting to swap bikes with seven laps to go and then being caught speeding in the pitlane.
Vinales had made his way to fifth place before crashing at the chicane.
"I can't explain what happened, because I don't even know why I crashed," he said. "I was pushing myself over the limit, trying to bring the Yamaha to the top and I think that if I hadn't crashed I could have reached the riders in front.
"It was everything or nothing and finally I got nothing."
(Reporting by Alan Baldwin in London, editing by Toby Davis and Ian Chadband)
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