The coach, whose side won 2-1 at home to go three points clear in La Liga, protested angrily on the touchline after the left back's studs-up tackle against the Argentine forward shortly before half time.
"Did you see my reaction? Then you can imagine what I was thinking. It shocked me but I am not going to go into details about it," he told a news conference at the Nou Camp.
Atletico's Argentine coach Diego Simeone refused to criticise Filipe Luis, however.
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"No not in any way," he told a news conference after being asked whether he was annoyed with the player. "It was an incident in the game and the referee interpreted it as he did.
"I am proud of the team that I have. They were impressive and played very well in the first half except for the 10 minutes when Barca pressed us. You can win or lose but if we lose I would prefer to do it this way."
The hard-fought top-of-the-table clash sent Barcelona clear of second placed Atletico with a game in hand.
Atletico had gone ahead through Koke and were causing Barca plenty of problems but their chances were hit by the dismissal of Filipe Luis as well as a red card for Diego Godin in the second half.
Barca had started slowly in recent victories over Malaga and Athletic Bilbao and they had to come from behind again with Messi and Luis Suarez scoring.
"We set out to attack but it didn’t go as we wanted," said Luis Enrique.
"It was a strange start where we struggled to get involved and we also conceded after making several mistakes, but we managed to turn it around and finish the first half well.
"After that our aim was to close the game down and despite the fact that we had one and then two players more the game remained open to the end. I am happy though the way the team battled against a team of this level."
(Reporting by Tim Hanlon, editing by Alan Baldwin)
