Since breaking away from Sudan in 2011, oil-producing South Sudan has struggled to assert control over remote territories, which are awash with weapons after a 1983-2005 war with the north.
Friday's attack was the worst violence in Jonglei State since 900 people were killed there in tribal attacks linked to cattle rustling in 2011, the United Nations said.
Rebels loyal to former theology student David Yau Yau and members of the Murle community killed 103 people, most of them women and children, in the ambush on ethnic Lou Nuer families, state governor Kuol Manyang said.
"They came under attack from people in a huge force," he said. "There are many children and women missing. Their fate is not yet known."
Fourteen soldiers escorting the convoy were also killed, he said.
The International Committee of the Red Cross said it had sent a medical team to treat the wounded.
Mr Yau Yau rebelled in July last year. He recruited armed youths antagonised by a government campaign to end tribal violence in Jonglei, which human rights groups say was marked by abuses by soldiers.