Barca had said Messi would miss the game with flu but was able to replace Pedro for the final half against a down trodden Osasuna.
“I didn’t vomit and there was no fever, I just had a stomach ache, nothing more,” Messi said.
“That’s why I couldn’t take part in this morning’s training but later on I recovered enough to be able to play.”
As long as next week’s second leg goes well, Barcelona FC have a quarter-final with rivals Real Madrid, who beat them 1-0 in last year’s final.
Real Madrid came back from two goals down to win against Malaga 3-2 on Tuesday.
Real Sociedad beat Real Mallorca 2-0 at their Anoeta stadium in San Sebastian earlier on Wednesday.
Mirandes took 2-0 over Racing Santander also Albacete, drew 0-0 at home to Athletic Bilbao.
Alcorcon beat Real Zaragoza at the last stage, a 2-1 win at home to Levante.
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