FIFA said Tuesday the Dutch federation must pay $14,480 after eight different players received yellow cards, including defender John Heitinga, who was booked a second time and sent off.
English referee Howard Webb showed five yellow cards to Spain, earning its federation a $9,650 fine.
FIFA's disciplinary code has a clause on team misconduct calling for a federation to be fined when at least five of its players are sanctioned in a match.
Spain won 1-0 in the July 11 final on Andres Iniesta's extra-time goal after the Netherlands was reduced to 10 players.
The match set a record for most cards received in a World Cup final, beating the six yellows shown when Argentina beat West Germany 3-2 in the 1986 final.
The final also was the worst behaved of the 64 matches played in South Africa. Chile and Switzerland players combined for nine yellows and a straight red card in a group-stage game.
FIFA paid Spain $30 million in prize money for winning the tournament, and the Netherlands was awarded $24 million as runner-up.