It was the Australian's 40th career victory and fourth consecutive win in Assen, giving him a 68-point championship lead over his Honda team- mate Alex Criville, who did not race after injuring his hand badly in a high-speed crash in Thursday's practice.
Doohan, who started from pole position, won both sections of the race which was split in two when rain prompted officials to call a halt with 11 laps completed.
Honda rider Carlos Checa, of Spain, who was in second place when the race was interrupted, came third in the second part of the 20-lap race to take second place overall ahead of Italian Aprilia rider Doriano Romboni.
"Conditions were definitely tricky today and had it not been for a five- minute delay for some reason we would have completed enough of the race distance in race one and we wouldn't have had to take so many risks in race two," Doohan said.
The fast changing weather conditions made it hard for riders to decide which tyres to put on for the second part of the race. "We had to take a gamble with an intermediate in the rear and a wet on the front," Doohan said.
In the 250cc class, Japan's Tetsuya Harada, riding an Aprilia, surged past Honda rider Ralf Waldmann, of Germany, in the final kilometre to win his second consecutive race. Waldmann snatched the championship lead from Italian Max Biaggi, who was disqualified for failing to comply with a stop-and-go penalty given after mechanics continued to work on his bike on the circuit less than three minutes before the start of the warm-up lap.
Italian teenager Valentino Rossi toyed with the opposition en route to his fifth victory of the season in the 125cc category to extend his championship lead to 33 points over Noboru Ueda of Japan.
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