Carragher was sent off for hurling a coin into the Highbury crowd after he was hit by the missile in the second half of a bad-tempered encounter.
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"Jamie says he was hit by a coin and other objects were thrown but you can't accept what he did."
Referee Mike Riley was left with little alternative but to dismiss the 24-year-old defender just seconds after goal-scorer Dennis Bergkamp had joined Martin Keown as Arsenal's second sending-off.
Carragher, who apologised for his actions, is now facing an FA and police investigation after a Scotland Yard spokeswoman confirmed that officers were probing the ugly incident. She said: "I cannot rule out charges but would not like to speculate on any offence which might have been committed."
Despite voicing his fears for players' safety after the latest outbreak of crowd violence, Thompson had no sympathy for his player.
"People throwing things worries me greatly but what Jamie did doesn't help matters.
"People see what is happening on television and they want to do it as well, and it has to be stopped because everyone has to take responsibility. I fear that one day a player will get seriously hurt, but I'm not looking to defend Jamie.
"You can't have that. Two wrongs don't make a right and I've told him.
"But I hope they don't make an example of him because our disciplinary record is one of the best in the Premiership."
Leeds official Riley will have his match report scrutinised at Soho Square today and Carragher is facing a lengthy ban.
Riley said: "It's an unfortunate incident. There was something thrown from the crowd and he was hit. Then he threw the object back and that's a case of violent conduct and he had to be sent off."
Carragher, 24 today, said: "I regret what happened because I let the club, the fans, my team-mates and myself down. No matter what the physical or verbal provocation, I shouldn't have reacted like that. I would like to apologise for any offence caused.
"I was frustrated and did it without thinking in the heat of the moment. Anyone who has seen me play regularly will realise it was completely out of character, but I'm not going to make excuses.
"I was wrong and as a professional football player I should have known better. It's a mistake I won't make again."
The England defender was the third player to go in a mad four-minute spell, which had earlier seen Keown become Arsenal's ninth sending-off this season for impeding Michael Owen when he was the last defender.
Bergkamp - scorer of a brilliant headed goal in the first half - followed when the red mist descended and he stamped on Carragher, sparking the disturbance in the crowd which led to the missile-throwing.
Gunners boss Arsene Wenger said: "I have to accept the referee's decisions. Dennis and Martin both felt they'd been harshly treated when they came off.
"But they were dismissals for trying to play football. We try to play football and don't try to kick people.
"I would pay to see a game like the one we played today if I was a neutral fan."