Spain managed to beat Holland 1-0 after an extra-time goal by Andres Iniesta.
Webb was forced to book 12 players and dismiss Dutchman Johnny Heitinga for two yellow cards.
“I don’t think the referee controlled the match well,” said Van Marwijk.
“Both sides committed fouls. That may be regrettable for a final. But the best team won the match.”
“We made a real game out of it and we had two great chances through Arjen,” explained Van Marwijk.
“I’m not someone to look back on the what the referee did. I think the best team usually wins the match.
“But if you look at the second chance of Robben, the referee should give Puyol a second yellow card, which would have meant him being sent off.
“It was a crucial moment just before the end of the 90 minutes. It is very bitter, but that is sport. It is harsh. And as I said, Spain were the better team.”