Belgian coach Marc Wilmots kept Lukaku on the bench until the 61st minute after the striker had already proven his form with four goals in the last two games, but the forward limped off just before full-time after sustaining an ankle injury.
"For now it looks like a severe sprain, but of course there will be further tests tomorrow," Wilmots said. "As it looks now, Romelu will be out for three or four days. Let's hope it stays that way."
The match was interrupted for around 40 minutes after a severe hail storm forced players off the field in the first half, while Tunisia were reduced to 10 men after 63 minutes when Issam Jemaa was sent off for a second yellow card for grabbing Vincent Kompany's shirt.
Belgium dominated but lacked the cutting edge and had only a few shots at goal until Dries Mertens slotted home in the 89th minute after being set up by Nacer Chadli's pass.
Belgium play Russia, South Korea and Algeria in Group H.