Messi was taken to hospital for tests after he hurt his left knee and came off in the eighth minute.
Messi walked off by himself as Munir El Haddadi replaced the four-time world player of the year in front of a quiet Camp Nou crowd of nearly 75,000.
“During preseason we had matches without Messi, Neymar, we used the same plan with other players”.
The win was just what Barcelona needed after they were thrashed 4-1 by Celta Vigo in midweek, but the victory was marred by the injury to Messi.
Messi faces “seven to eight weeks” on the sidelines, but Enrique has promised to overcome the 28-year-old’s absence.
He added: “Now we’re thinking about our next match in the Champions League”.
Rakitic has refused to play down the loss of the forward, but has insisted that the Catalan club will “fight together” to get through the period without the 28-year-old.
“It’s always a bad thing when a player gets injured”, Hernandez told Spanish sports daily Marca on Monday.
Messi will also not be able to lead the Argentine national side for the first South American elimination rounds for the World Cup, against Ecuador, Paraguay, Brazil and Colombia.
Overall, his exploits accounted for more than a third of the team’s goals in the last league and Champions League season. Barcelona have enviable strength in depth in attacking positions, however, and boss Luis Enrique insists that it is now up to the team to compensate for his absence.
The club can field Arda Turan and fellow new arrival Aleix Vidal after the ban on its new players expires in January.
With Messi expected to be out until the end of November, Barca head coach Luis Enrique will need to find a way to make up for his production on the pitch.
“Being a strong team is Europe must be our target”, City coach Manuel Pellegrini said.
Messi was injured as he tried to turn the ball home after taking a wonderful first touch inside the area.