Waris tucked in from close range in the 36th minute after goalkeeper Hugosson had made double saves.
Rene Makondele opened the scoring on 17 minutes from the spot before the Ghana international doubled the lead.
Makondele added the third in the 45th minute.
Last week, Waris was on target as they defeated newly promoted Atvidaberg 3-0.
He is the second top-scorer in the Swedish top-flight.
Watch video of Waris’ goal against Gefle below