Gunners skipper William Gallas bundled in from close range with just two minutes left to cancel out a controversial penalty from Ismael Bangoura after full-back Bacary Sagna was adjudged to have pushed over Ognjen Vukojevic.
However, Wenger felt there should have been more time for his men to go on and win the tie - which would have been a first European victory in the former Soviet Union.
The Arsenal manager confronted the referee following the final whistle, which he believed came too soon.
"I wanted to understand how we played only three minutes of injury-time, and then only had one minute," said Wenger.
"Every referee looks to have a different computer to calculate the in time and still I do not know and really understand how it works.
"It looks like through inspiration of the referee, and he could not explain it. He just said it was enough."
Wenger continued: "When he got to 1-1, there was no game any more.
"We were on top, they looked very tired, but the game was finished because of the interruptions for injuries and stoppages.
"You could feel the game was there for the taking, but we had no more opportunity to play."
The Arsenal manager also rejected suggestions from Ukrainian journalists the referee had allowed Gallas's effort to stand even though he was offside - and hit out at the official again for not protecting winger Theo Walcott more from some heavy tackling.
Wenger said: "We do not want to score offside goals, but this is the same referee who should have sent off the left-back three times at least during the game because he destroyed Walcott.
"And it is the same referee who gave Kiev a penalty which you did not complain about."
Wenger reflected: "The game is a mixture of frustration and relief.
"The game should be over at half-time because we had clear chances in the first half, but it is a relief because with three minutes to go we were 1-0 down.
"I felt our level dropped in second half and we did not create as many chances as we would have liked.
"We feel we have lost two points today."