The match at the Vicente Calderon was heading towards a draw after Daniel Alves and Radamel Falcao had traded strikes, but the Ballon d'Or winner popped up with a sublime free kick to earn all three points late in the game.
"Results are always fair. We tried to play the game in a specific way and close down the spaces," the coach stated.
"In the first half it was difficult for us and in the second half the game was more open. We could have taken the lead, but a genius [Messi] left us with nothing.
"The referee was did well, although there were some little issues," concluded the coach.
Atletico Madrid are ninth in the La Liga standings with 38 points, and travel to Sevilla in a week's time.
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