A UEFA spokesman told Reuters that European soccer's governing body had been alerted to heavy and unusual betting on the second leg of the first round tie.
The match in question saw first-time European participants Honka winning 4-2 away on July 1 after holding TVMK to a 0-0 draw in the first leg.
Honka were themselves eliminated in the competition's second round after losing on the away goals rule to Danish side AaB.
The spokesman said the matter had now been passed to UEFA's disciplinary unit with no particular timeframe set for the investigation.
In Estonia, media reported that there was "lively betting" on the game, with considerable sums wagered on a Honka victory.
Postimees newspaper reported that UEFA suspected TVMK of losing the game on purpose.
"Let them investigate if they wish. Fraud with the totaliser is not our problem," Postimees quoted TVMK president Piotr Sedin saying.
Aivar Pokhlak, the head of the Estonian FA agreed. "We have very little information at the moment and what we have is unofficial.
"However, Estonian football and TVMK should feel no shame. "We know where the bets were made from. I cannot say which country it was from, but it was not from Estonia," Postimees quoted him as saying.
This incident is the second to blight the relatively low key Intertoto Cup this season.
UEFA kicked Polish club Legia Warsaw out of the cup and banned them from European competition for two seasons earlier this month after their fans rioted during a second round, first leg match against Vetra Vilnius of Lithuania on July 8.