Bavuma has been a key part of South Africa's middle order in recent years and his return is a boost for the side as they seek to earn a place in the World Test Championship (WTC) final at Lord's next year.
Allrounder Marco Jansen (rested) and fast bowler Gerald Coetzee (injury) are also back in the squad after missing the comprehensive win in Bangladesh.
"We've picked the strongest possible side to ensure we stay competitive and keep our hopes alive for a place in the World Test Championship final," coach Shukri Conrad said.
"We've named a squad of 14 instead of the usual 15 to allow players on the periphery of selection the opportunity to play first-class cricket for their respective provincial teams.
"It's great to have Temba back leading the side after his recovery. His leadership and skill are invaluable to the team."
Australia and India are the top two in the WTC and South Africa will likely have to win both matches against Sri Lanka, and two home Tests against Pakistan to reach the final.
South Africa Squad:
Temba Bavuma (capt), David Bedingham, Gerald Coetzee, Tony de Zorzi, Marco Jansen, Keshav Maharaj, Aiden Markram, Wiaan Mulder, Senuran Muthusamy, Dane Paterson, Kagiso Rabada, Tristan Stubbs, Ryan Rickelton and Kyle Verreynne.
