The method under which the team that scores the most goals away from home wins the tie was introduced in the mid-1960s.
It replaced the coin toss or the drawing of lots to settle ties which were level on aggregate after the second leg.
The system is used in the Champions League and Europa League plus many other domestic cup competitions around the world.
But in Blatter's column in the FIFA Weekly magazine, which is published on Friday, he writes that the rule favours teams playing away from home in the second leg because those games can go to extra time meaning more chance of scoring an away goal.
"It is time to rethink the system," says Blatter. "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.
"Such an imbalance has already been disposed of in various competitions. The away goals rule is no longer used in the semi-finals of the promotion playoffs in English football."
Blatter suggests 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.
The away team has then done enough to force extra time and away goals do not count double in the additional 30 minutes.
(Editing by Ken Ferris)
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