The Spanish defender, already booked in the first half, committed a foul on the Dutch winger 10 minutes from time when he sped past him but Robben continued and was denied by goalkeeper Iker Casillas.
"When I got my second chance the referee should have given us a free-kick and Puyol a (second) yellow card," Robben told reporters.
"He gave the advantage but there was none as I could hardly move and the goalkeeper was too close already."
After beating Brazil in the quarter-final, Robben was widely criticised for his diving but in the final he stood firm instead of making clear to the referee that he had been fouled.
"As a player you always want to go on and especially 10 minutes before time in a World Cup final when you are heading towards the goal," he added.
"When I missed my first chance it was simply my error - I was not patient enough and should have gone around him instead of this poor finish," he said of his 62nd minute opportunity when he broke through from a superb pass from Wesley Sneijder.
The Dutch afterwards said they were less than impressed with the referee's performance during the final.
Webb showed eight Dutch players a yellow card and sent off Netherlands defender John Heitinga in the first half of extra time.
"When you play a World Cup final you need also a world class referee and - I have to be careful what I say - this was not the case for this match," Robben added.
However, the winger was lucky himself not to be dismissed after deliberately playing on after the whistle had blown for an infringement. It would have been his second yellow card but Webb simply admonished him.
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