The Dutch side beat Celtic 1-0 on November 6 to leapfrog them into third place in Group H of the Champions League, midfielder Lasse Schone netting the only goal of the game.
However, the defending Eredivisie champions have been hit with the sanction after the governing body found that their supporters had been guilty of improper conduct by unfurling the banner at the Amsterdam Arena.
A statement on the Ajax website read: "Ajax have been fined by UEFA after a banner appeared on the stands of the Amsterdam ArenA during the match against Celtic FC.
"The banner was aimed at Ajax's opponents that night. UEFA imposed a fine of 25,000 euros.
"The possible penalty for such an offense is a fine of 50,000 euros plus the closure of some parts of the stadium at the next European home game.
"After a prompt and adequate response from Ajax the fine was halved and the partial closure averted. The penalty will be recovered from those responsible."
Ajax could be punished further following crowd trouble during their visit to Celtic on October 22.
Another disciplinary hearing is set to take place next week, with a ruling expected on November 21.
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