Rookie Crutchlow, riding in his first race since breaking his collarbone two weeks' ago at Silverstone, was forced to pit from fifth with a front tyre problem. The Englishman rejoined to finish 14th and last.
After the first lap incident, reigning world champion Lorenzo mounted a charge through the field, reaching sixth by the flag - but he has dropped from 18 to 28 points behind Stoner.
Simoncelli was slower to restart, but eventually fired his RC212V back into life and was credited with ninth place.
Rossi's team-mate Nicky Hayden, riding on the standard GP11 but with a new chassis, finished between Rossi and Lorenzo, with Colin Edwards in seventh for Tech 3.
With Dani Pedrosa absent for a third race in a row, HRC promoted Hiroshi Aoyama to the Repsol squad this weekend, with factory test rider Kousuke Akiyoshi filling in for Aoyama at Gresini. Aoyama claimed eighth place, with Akiyoshi 13th.
Pramac Ducati's Loris Capirossi missed the race after dislocating his right shoulder in qualifying. Team-mate Randy de Puniet crashed out in the early stages of the race, as did rookie Karel Abraham (Cardion AB Ducati).
The Dutch TT has taken place every year since 1925, with the exception of 1940-1945 because of the Second World War.
The race - always held on the last Saturday in June - formed part of the original 1949 FIM Road Racing World Championships and Assen has continued to host the Dutch round ever since. Assen is the only circuit to have remained on the calendar since 1949.
Lorenzo and Spies were both using a special livery to celebrate the 50th anniversary of Yamaha's involvement in grand prix racing.
The Italian Grand Prix at Mugello - the home race for Valentino Rossi and Ducati - takes place next weekend.