Messi escapes fractured ankle
World Player of the Year Messi, who scored Barca's opening goal, clashed with Atletico defender Tomas Ujfalusi in stoppage time at the Calderon and clutched his face with both hands as he was carried round the touchline.
Barca said in a statement on their website he had sprained the external ligament in his right ankle but there was no bone damage and further tests would be conducted on Monday.
"We are very pleased with the win but sad about the injury to Leo (Messi)," Guardiola told a news conference.
"In principle, a fracture is ruled out which was what was worrying us," he added. "Tomorrow we'll do some tests and they'll tell us how he is."
Ujfalusi had already been shown a yellow card and received a straight red for the challenge.
"The video images speak for themselves I imagine," Guardiola said when asked about the tackle.