Atletico right-back Juanfran was penalised for kicking Sergio Busquets inside the area late on and Messi was relieved to slot home the rebound after seeing his penalty saved smartly by Jan Oblak.
The two sides will meet again at the Vicente Calderon in Madrid on January 28, with a draw enough for the Catalonians to progress, while an away goal would mean that Atletico have to score thrice in normal time if they are to progress.
However, despite the positive result, Barcelona midfielder Andres Iniesta stressed that the tie is only half finished but was happy that his side did not concede an away goal.
“It's a good result, but we've got the return leg to go and that will be another intense 90 minutes," said Iniesta. “We've put in a great shift against a team that's really difficult to overcome. We're happy to win 1-0. Keeping a clean sheet is very important, but it doesn't guarantee anything.”
On the other hand, Atletico boss Diego Simeone remains confident that his side's tremendous home form can see them turn the tie on its head.
"We still have a chance against an opponent that played very well. The tie is still very open," he said.
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