With the score level at 0-0 four minutes from the end and about to go to a penalty shootout and Netherlands down to 10 men, Iniesta scored from close range after a Cesc Fabregas pass to end the all-European final.
Spain had the best of the play in a bruising game in which nine players were shown yellow cards by English referee Howard Webb in the first 90 minutes, a World Cup final record.
Dutch defender John Heitinga was sent off for a second yellow in the second half of extra time.
Neither team has won the World Cup before though the Dutch were playing in their third final.
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