The firm and seven distributors have been found guilty by commission anti-trust officials of attempting to keep prices artificially high in some EU states between 1991 and 1998.
The severity of the fine, the fourth highest ever meted out by commission trade watchdogs for a single offence, reflected Nintendo's role as "the driving force behind the illicit behaviour", the commission said.
The distributors, including Scotland-based John Menzies, were fined 18m euros.
Appeal
But Nintendo said it would fight the penalty.
"In view of the size of the fine, which Nintendo finds surprising, Nintendo will lodge an appeal," the company said.
While accepting that it had broken EU rules, the firm said it had reformed its practices.
John Menzies, which said its fine of £5.4m was "totally disproportionate", said it was considering legal options.
The firm was implicated through its THE Games unit between 1995 and 1997.
"We feel that the commission has not fully recognised... [its] earlier acceptance that this was a mistake, not a deliberate transgression; that THE Games was more victim than villain," Menzies chief executive, David Mackay said.
Price differences
The fines follow a two-year probe by the commission into claims that Nintendo prevented distributors from selling goods from low-cost countries in states where prices were higher.
Prices of Nintendo products were up to 65% higher in Germany or the Netherlands than in Britain.
"Every year, millions of European families spend large amounts of money on video games," Competition Commissioner Mario Monti said.
"They have the right to buy the games and consoles at the lowest price the market can possibly offer.
"We will not tolerate... behaviour intended to keep prices artificially high in the European single market."