"It was violent play and therefore he got a red card," said the Argentine referee Horacio Elizondo referring to the Manchester United player’s stamp on Ricardo Carvalho.
Speaking to English newspaper, The Times, he also denied being influenced by Portugese midfielder Cristiano Ronaldo.
"People can say what they want, but this had absolutely no influence," he said.
"For me it was a clear red card, so I didn't react to the Portuguese players. There was pushing and shoving on both sides, but for me it wasn't a reason to caution anybody."
Overall, Elizondo said he was "very satisfied with the spirit of fair play" in the match and that England coach Sven Goran Eriksson had congratulated him for an "excellent performance".
"He said that I was right to send off Rooney because it was rough play."
Meanwhile, Wayne Rooney has released a statement on the incident after claiming he was “gobsmacked” by his red card.
"I'm bitterly disappointed to have been sent off in a World Cup finals match for England," the 20 year old said in a prepared statement."I remember the incident clearly and have seen it several times since on television. I am of the same opinion now as I was at the time that what happened didn't warrant a red card.
"If anything, I feel we should have had a free kick for the fouls committed on me during the same incident.
"I want to say absolutely categorically that I did not intentionally put my foot down on Ricardo Carvalho. He slid in from behind me and unfortunately ended up in a positioning where my foot was inevitably going to end up as I kept my balance. That's all there was to it.
"If you ask any player -- and indeed almost any fan -- they will tell you that I am straight and honest in the way I play.
"From what I've seen in the World Cup, most players would have gone to ground at the slightest contact but my only thought then was to keep possession for England."
FIFA had given the English forward until Thursday to explain his actions.