The long-serving central defender was withdrawn 12 minutes into the second half in Wednesday's 4-1 Copa del Rey quarter-final first-leg win at Levante, having taken a knock to his left leg.
Puyol's injury was assessed on Thursday and, although he has not sustained serious damage, the Barca stalwart may not feature this weekend.
A statement on the Catalan club's official website said: "Carles Puyol limped off during last night's game against Levante after a knock on his left leg, which Club doctors examined this morning, before confirming the bruising will make him a doubt for Sunday's game against Malaga.
"The club captain was substituted on 57 minutes after clashing with Levante forward Barral.
"Club doctors treated him pitchside, but he was able to limp back to the changing rooms before being replaced by Javier Mascherano."
Barca have drawn their last two La Liga games and will be eager to get back on track in defence of their title by beating Malaga.
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