The English referee did not show a second yellow card to Spain defender Carles Puyol when he appeared to impede Arjen Robben in the 82nd minute, allowing Robben to play on and attempt to score.
Webb, who also refereed the Champions League final, said before the game he wanted to have a calming influence on the action.
He described his perfect game as one when "nobody is speaking about the officials, and they are speaking about the excellent game of football and the skill of the players." That's not how the biggest game of his career worked out.
The 14 yellow cards, one leading to a red, was a record for a World Cup final, beating the six collected by Argentina and West Germany players in 1986 At the final whistle, Netherlands midfielders Mark Van Bommel and Wesley Sneijder headed directly toward the 38-year-old former policeman.
Robben, who was booked for protesting that he was fouled by Puyol, joined in as defender Joris Mathijsen rushed over to gesticulate angrily at the referee.
Webb was subjected to more Dutch derision when he went to collect his cup final medal.
A chorus of jeers and whistles rained down from the stands when Webb led his assistants Darren Cann and Mike Mullarkey to receive their gifts from South Africa President Jacob Zuma and FIFA president Sepp Blatter.
Webb brandished his first yellow card in the 15th minute when Netherlands forward Robin van Persie caught Spain left back Joan Capdevila with a late challenge, as the Dutch team tried to break up Spain's rhythmic passing style.
So began a tit-for-tat exchange of five bookings in 13 minutes as Van Bommel, teammate Nigel De Jong, Spain defenders Sergio Ramos and Puyol also went into Webb's book.
In the second half, the snappy, scrappy pattern of play continued and so, therefore, did the yellow cards.
Dutch captain Giovanni van Bronckhorst and Heitinga were next, then Capdevila for fouling Robben.
Robben was the next to see yellow when he furiously chased after Webb, believing he should have been awarded a free kick and Puyol sent off.
In a similar breakaway in the second period of extra time, Heitinga leaned his arm across Fernando Torres to earn his second yellow.
It was the first time Webb had produced a red card at this World Cup in his fourth match.
Webb was awarded control of the final after near-faultless handling of three previous games in which he showed 17 yellow cards.
He was widely praised for his player-management skills while showing four yellows to each team in a tense group match when Slovakia eliminated defending champion Italy with a 3-2 victory.
