Al Shabaab made no immediate comment and there was no word from the United States, which has launched drone strikes in the past that have killed senior officials in the al Qaeda-affiliated group.
Residents said the attack took place at sunset around the village of Abaq Xaluul, about 25 km (16 miles) outside the town of Baardheere in the southern part of Somalia. Baardheere lies about 300 km (190 miles) east of Mogadishu.
"I was on the outskirts of Abaq Xaluul village when a car drove past me and soon I heard the huge blast from a drone ahead of me," resident Hussein Nur told Reuters by telephone.
"I saw the car and the three men on board completely burnt and then many armed al Shabaab fighters driving in cars reached the scene," he said.
Another resident from Baradheere, Ahmed Farah, gave a similar account, saying the three men in the car had been al Shabaab fighters. He did not identify them or say if they were senior al Shabaab members.
Last year, a U.S. unmanned aircraft killed Ahmed Godane, the then leader of al Shabaab, forcing the group to appoint a new chief. Last month, a U.S. missile strike killed Yusef Dheeq, blamed for masterminding attacks at home and abroad.
Al Shabaab has also been under pressure from a ground offensive of African Union peacekeeping troops and Somali soldiers which has driven the group out of strongholds, but it still holds smaller settlements and some rural areas.
Despite the setbacks, the group has continued to make bomb and gun attacks in the capital Mogadishu and other towns, including Baidoa, where it attacked a regional government headquarters on Thursday.