Clarke missed Australia's first two games - a 198-run win over Zimbabwe and a seven-wicket loss to South Africa - after incurring a hamstring injury during a training session.
However, after a week of extensive rehab Clarke was one of three changes to the Australian side, who recalled off spinner Nathan Lyon and gave a first game to seamer Ben Cutting.
Steve Smith was the batsman to make way, while fast bowler Mitchell Johnson was rested and Kane Richardson dropped out.
While captains generally elect to bowl first at Harare Sports Club, Clarke suggested he wanted his side to defend a total better than they had against South Africa, who chased down a target of 328 with 20 balls to spare on Wednesday.
Zimbabwe made one change to their side, with left-arm seamer Brian Vitori replaced by Donald Tiripano.
Teams:
Zimbabwe: Tino Mawoyo, Sikandar Raza Butt, Hamilton Masakadza, Brendan Taylor (wk), Sean Williams, Elton Chigumbura (capt), Malcolm Waller, Prosper Utseya, Donald Tiripano, John Nyumbu, Tendai Chatara.
Australia: Aaron Finch, Phillip Hughes, Michael Clarke (capt), George Bailey, Glenn Maxwell, Mitchell Marsh, Brad Haddin (wk), James Faulkner, Mitchell Starc, Ben Cutting, Nathan Lyon.