The Argentinean entered the game as a 63rd minute substitute for his first appearance since tearing his hamstring away to Betis Nov 10 last year, reports Xinhua.
Messi's goals came in the last minute of the game following great work between Sergio Busquets and Martin Montoya left him with a simple tap.
If his first goal was simple, the second, which came with the last kick of the game was a trademark goal from the striker.
By the time Messi got into the game, his side were two goals ahead thanks to Cesc Fabrigas, who opened the scoring after just nine minutes and added second from the penalty spot moments.
It was a fine display from Cesc, but the last four minutes meant it was Messi who captured the headlines.