Messi played the full game at Balaidos as Barca won 1-0 despite having missed Argentina's friendlies against El Salvador and Ecuador during the international break due to foot problems.
Barca had hinted the forward was likely to feature in Sunday's clash and Luis Enrique insisted there was no concerns surrounding his appearance.
Asked whether Wednesday's clash with Almeria was an ideal time to give Messi a rest, he explained: "Maybe it is, maybe not.
"We know what condition our players are in and I can guarantee we do everything to care for the players.
"We don't run risks regarding injuries but what I will say is Barca fans, don't worry. We know what we're doing with our players.
"We get rumours that people like to stir up but I don't have anything to say about that."
Barca's win at the weekend leaves them four points clear of Real Madrid going into the final nine games.
With sections of the Madrid press urging talk of a resurrection for Real's title bid after their 9-1 win over Granada, Luis Enrique added: "What is said in the press doesn't concern us.
"We're in a very privileged position but the tournament has varied over the course of the season. We're in a strong position but we need to keep doing our job. As long as we win teams can't catch us up.
"If you think too far ahead you tend to forget about the task at hand. We need to repeat what we've been doing all season against Almeria.
"It's a very crucial game for winning the league, I'm going to need 11 great players, I want to put out 11 players that guarantee three points."
