European champions, Barcelona got their bid to defend their La Liga title to a winning start when Luis Suarez buried a fine volley shortly after halftime to secure a hard-fought 1-0 win at Athletic Bilbao on Sunday.
But the treble winners, who cannot sign players until January, lost full-back Dani Alves and midfielder Sergio Busquets to injury.
Messi’s penalty kick was saved by Gorka Iraizoz after Gorka Elustondo was deemed to have fouled Suarez.
After the break, Suarez scored the winner from Jordi Alba’s cross.
It was the first time in three years the Uruguayan has been able to start a season following biting bans in the past two years.
But Luis Enrique, who has lost Pedro and Xavi from his squad this summer, will be worried about injuries to right-back Alves and midfielder, Busquets.
Barca are not allowed to register Arda Turan or Aleix Vidal or any other summer signings they make until January because of a transfer ban.
The game will be seen as revenge for Barcelona, who lost 5-1 to Athletic Bilbao over two legs in the Spanish Super Cup in the past two weeks.
Sergi Roberto, who had a fine game at right back after replacing Alves in the 19th minute, cracked a shot against the frame of the goal on the hour before Barca coach Luis Enrique had to make another change when Busquets appeared to damage an ankle in a clash with Bilbao striker Aritz Aduriz.
The Spain international was taken off on a stretcher although his coach later said neither his injury, nor that of Alves who looked to have tweaked a groin muscle, appeared to be serious.
“We know that these kinds of matches give us strength in our effort to win La Liga,” Suarez told Spanish television.
“We also knew that they would be a very difficult, very tough opponent,” added the Uruguay striker.