Webb brandished 14 yellow cards and one red - a record for a final - in a fiery encounter which saw Andres Iniesta's extra-time goal secure a 1-0 win for Spain.
The South Yorkshire official was booed by Dutch fans at the final whistle and Liverpool forward Kuyt said: "We are angry that we lost because we came so close. I know you cannot blame others, but the referee favoured Spain.
"We had many more yellow cards than we deserved. That ultimately cost us the cup."
Holland coach Bert van Marwijk suggested Webb might have been influenced by Spanish media blaming the referee for Spain's defeat by Switzerland in their opening match.
The Holland coach said: "I don't think the referee controlled the match well. But let me be clear about this: the best team won the match.
"I'm trying to analyse the match as best as possible. But I read a few things today about how angry Spain were at the refereeing in the first match against Switzerland.
"If you view the performance (of the referee) today, you'd almost think now that that first match had an influence on this game now."
Van Marwijk admitted some fouls had been "terrible" but said both sides were responsible, although challenges by Nigel de Jong and Mark van Bommel were particularly X-rated.
He added: "It's not our style. Let me put it this way, it's not our style to commit horrible fouls. It's not our kind of football.
"It was a World Cup final and people were tense. Look at the rest of the tournament. I think both sides, also the Spaniards, committed terrible fouls.
"I'm on the bench and I haven't seen any replays. I'd have to see the replays. The way I saw it from the bench was very different."
Van Marwijk said the Dutch had done well to reach the final and could have won it.
He continued: "No-one expected us to be here, in the final. We came very close to a penalty shoot-out. We could even have scored through Robben.
"Whether we would have deserved that, I don't know. But it's a final. It's very disappointing. You want to win it, and we might have done. I think we performed really, really well to get this far."
Van Marwijk also defended Holland's attempt to 'win ugly' and said that had not been the plan from the start.
He added: "It was still our intention to play beautiful football, but we were facing a very good opponent.
"Spain are the best footballing country in the past few years, so we needed to have a top day to beat them.
"We did a good job tactically on them. We got into good positions at times. Both sides committed fouls. That may be regrettable for a final. It's not our style, but you play a match to win.
"It's a World Cup final, and there's a lot of emotion out there. You saw that with both teams. I'd loved to have won that match, even with not so beautiful football."