Wenger is not the first to call for the rule to be changed -- FIFA president Sepp Blatter expressed the same view last October saying it had "fallen behind the times."
Arsenal and Premier League rivals Chelsea, were both eliminated on away goals in the last 16 of the competition after drawing 3-3 with French League teams.
Chelsea drew 1-1 at Paris St Germain but were eliminated after a 2-2 draw at Stamford Bridge, while Arsenal lost 3-1 at home and went out despite winning 2-0 at Monaco on Tuesday.
In his pre-match briefing before Arsenal face Newcastle United in the Premier League on Saturday, Wenger said the time had come for the rule to be changed.
"I think it should be questioned. It's a rule that is outdated now and should be changed.
"None of the teams in the competition apart from Barcelona looks to be superior in Europe today.
"Maybe the rule should count after extra time. This rule was created in the 1960s to favour teams to attack away from home but since then football has changed and the weight of the away goal is too big today."
The away goals rule replaced the coin toss or the drawing of lots to settle ties which were level on aggregate after the second leg.
Last October Blatter wrote in his column in the FIFA Weekly magazine, "It is time to rethink the system.
"Football has progressed since the 1960s, so the away goals rule may now be questioned. Does the away goals rule still make sense?
"The idea dates back to a time when away games were often an adventure, involving journeys that could be long and arduous -- and the playing conditions would vary considerably.
"In reality it favours the club that play away from home in the second leg. Where the scores are tied, that team has 30 minutes more than their opponent to score a valuable away goal. After all, in the first leg there is no extra time."
Blatter suggested implementing the rule used in the MLS playoffs in the United States and in the CONCACAF Champions League where away goals only count "double" until the end of normal time.
(Reporting by Mike Collett; editing by Amlan Chakraborty)
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