Spaniard Andres Iniesta dashed Dutch World Cup hopes for the third time, after they lost the 1974 and 1978 finals, when he scored the winner in their 1-0 victory with four minutes left to play in extra time.
"It is very bitter, very sad, but that is sport," said Van Marwijk. "It is harsh but the best team won tonight."
In a rough final that saw a record 13 yellow cards and one red card for Dutch defender John Heitinga, Netherlands had their chances but twice winger Arjen Robben failed to score from close range.
"You could feel from the start the team that would score the first goal would also win the match. Those chances from Robben could have meant victory but unfortunately we were not lucky," he said.
"Nobody expected that we would have been here, playing the final, and we came so very, very close to the penalty shootout," said the coach. "We were unlucky."
"If we deserved it, I do not know. It is disappointing. We came so close and we really wanted to win. We could have with a bit of luck."
Instead of Netherlands lifting their first World Cup it was Spain, appearing in their first final, who became the second team after West Germany in 1974 to follow up winning the European Championship by lifting the biggest prize of all.
France, who won the World Cup in 1998, did it the other way around, claiming the European title in 2000.
Van Marwijk refused to blame referee Howard Webb for his team's defeat although he did say the Englishman did not have a firm grip on the match.
"I do not think the referee controlled the match well but let me be clear: the best team won," Van Marwijk said.
"Both sides committed fouls and it may be regrettable for a final and it is not our style but you do play a match to win.
"I would have loved to win the match even with not so beautiful football," he said.
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