Messi had to come off at halftime in last weekend's 6-0 demolition of Athletic Bilbao at the Nou Camp and missed Wednesday's 2-1 King's Cup quarter-final first leg victory at the Basque club.
The FIFA Ballon d'Or holder complained of lingering discomfort and was rested as a precaution. A hamstring strain was ruled out.
Neymar was not included in the squad for the match at Malaga's La Rosaleda stadium due to a similar complaint, Barca said in a statement on their website.
"Tests conducted this afternoon ruled out an injury in the (hamstring) area and his recovery will determine when he can play again," they added.
Barca coach Luis Enrique said Messi and defender Jeremy Mathieu, who has been sidelined with a calf problem, would probably be available for the game at on the south coast.
"They have trained and we will see how (this evening's) session goes," he told a news conference. "I don't think there will be any problems."
A win for Barca, who have a game in hand over their main rivals, would put them a point clear of Atletico Madrid at the top of La Liga.
However, Luis Enrique said he was wary of Malaga, who have made life difficult for Barca in recent meetings in Spain's top flight.
The Qatar-owned club, who are 12th with just over half the season played, held Barca to a 0-0 draw in Malaga and beat them 1-0 at the Nou Camp last season while the champions edged a 1-0 win at home in August.
"Malaga are one of the opponents we have struggled to beat, both last season and this year," Luis Enrique told reporters.
"They created chances against us and caused us problems when we were trying to go forward," added the former Barca and Spain midfielder, who was a team mate of Malaga coach Javi Gracia in the Spain Under-21 side.
Atletico, who are two points clear of Barca at the top, host Sevilla and Real Madrid, two points adrift of the champions in third, play at Real Betis on Sunday.
(Reporting by Iain Rogers; Editing by Janet Lawrence)
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