The upper section of the Richard Donald Stand - officially opened by Princess Anne in 1993 - will be sectioned off and fans moved to other parts of the ground.
The club would consider reopening the upper tier for selected fixtures throughout the season should there be sufficient demand to do so.
A spokesman said: "The club recently conducted a supporters survey and the overall response from the vast majority of supporters contacted was that they would be willing to relocate.
"As a result the club has taken the decision to close the RDS Upper Deck for the 2013/2014 season.
"With almost three quarters of Aberdeen fans stating they would like to sit in the more heavily populated areas of Pittodrie Stadium, we hope this move will encourage the migration of our supporters to areas of the stadium which are less concentrated.
"Aberdeen FC is committed to making the match-day experience a memorable one for our dedicated supporters.
"We want Pittodrie to become a 'fortress' again and for the Red Army to be united in voice as they back the team on a match-day."