World number three Medvedev walked off court at the end of the match examining his hand before pointing his middle finger at the stands.
The former US Open champion Medvedev, renowned for his on-court outbursts, was booed by the crowd during the second set for throwing his racket before receiving a code violation for delaying the match when he sat down in protest.
"No, I didn't (give my middle finger to the crowd), I just checked my nails," Medvedev told reporters.
"It's nothing more than that. Why would I do that to this beautiful crowd in Paris?
"The crowd didn't stop booing. I have a lot of French friends and they don't seem to like very much this tournament. Maybe there is a reason. I played much better here without the crowd," added Medvedev, who won in Paris in 2020 during the COVID-19 pandemic.
World number 17 Bulgarian Dimitrov hit 48 winners and needed seven match points to reach the third round in Paris, a week after Medvedev beat him in the second round of the Vienna Open.