Espanyol's academy graduate Oscar Melendo crashed in the only goal of the game in the88th minute after Messi had his spot-kick turned away by former Real Madrid goalkeeper Diego Lopez earlier in the second half.
Melendo, 20, came on as a second-half substitute and picked the right time to score his first senior goal for the other Barcelona-based club.
"We have several players injured and he's training well".
Barcelona hadn't lost since a 2-0 defeat by Real Madrid in the second leg of the Spanish Super Cup on Aug 16.More news: CPU Bugs 'Meltdown' and 'Spectre' Threaten Systems
Umtiti has become a key player for the La Liga giants since moving to the Nou Camp from Lyon in the summer of 2016. "We were playing too defensively".
The injuries are piling up for Ernesto Valverde as Samuel Umtiti, Paco Alcacer and Philippe Coutinho are still not ready to return to the Barcelona squad. It was hard for us, but we had it under control.
"But we weren't efficient in the final third and then, after the missed penalty, the crowd reacted and came alive".
"We played with the same players in Vigo [against Celta] and I am happy with them", the coach said.
"We are in good shape to play Barcelona - if we could choose one, it would be this one".