After Dinamo beat Arsenal 2-1 in their opening Champions League Group F match in September, midfielder Arijan Aremi tested positive and was banned for four years. The club are appealing.
Under UEFA rules the result of a match stands if only one player fails a test.
"You cannot say 'okay, they had a doped player and the result stands'" Wenger told reporters ahead of Tuesday's return match in London.
"That means you basically accept doping.
"If doesn't look logical, especially if you (test) only three players."
Last week Wenger called for more blood testing in football.
The following day, he said, UEFA testers visited the club's training ground for the first time he could remember in his 19 years as Arsenal manager.
Dinamo's manager Zoran Mamic said it was fair that the win should count.
"Mr Wenger can talk about what he wants but there are other people who make decisions about that," he told a news conference.
"I don't think there is a problem with doping in football."
Arsenal need to win on Tuesday and hope Olympiakos Piraeus lose against Bayern Munich to have any chance of qualifying for the knockout stage of the competition, which they have done for 15 years in succession.
(Reporting by Steve Tongue; editing by Justin Palmer)
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