Clarke will bat at number three as Steve Smith sits out with Phil Hughes retained as opener.
Clarke admitted Smith would feel hurt by his omission.
“He hasn’t had much of an opportunity in this series batting at six and seven, but he was picked in the (tournament’s) first squad as well so he’ll obviously be very disappointed,” Clarke told reporters at Saturday’s training session.
“But I got back in the team and someone had to go.”
Mitchell Marsh will drop down the batting order to six but will probably get a chance to bowl with the new ball as Mitchell Johnson is being rested.
All rounder Ben Cutting, who played the last of his three ODIs more than 18 months ago, will play his first match of the series at the expense of Kane Richardson.
Nathan Lyon, who missed Wednesday’s seven-wicket defeat by South Africa, was recalled for the match that will take place on spin-friendly conditions at the Harare Sports Club.
Clarke suffered a left hamstring strain during his first training session in Zimbabwe last week and missed the 198-run victory over the hosts on Monday and the defeat by South Africa in the opening encounters of the triangular series.
The 33-year-old, who is desperate to return to competitive cricket after a four-month break, endured intensive physiotherapy to regain match fitness.
Team: Aaron Finch, Phil Hughes, Michael Clarke (captain), George Bailey, Glenn Maxwell, Mitchell Marsh, Brad Haddin (wicketkeeper), James Faulkner, Ben Cutting, Mitchell Starc, Nathan Lyon.
(Reporting by Mark Gleeson, editing by Pritha Sarkar)