He was struck in the head during the first meeting on Thursday, which Zimbabwe won by five wickets to take a 1-0 lead in the three-match series.
"Ballance had mild concussion symptoms and, as a precaution, we recommended he be rested in order for him to fully recover," said Zimbabwe team doctor Solomon Madzogo.
The batter made his debut for the country of his birth this week having played Test and one-day internationals for England over five years from 2013.
Ballance was released by English county Yorkshire last year after admitting he used racist language against teammate Azeem Rafiq. He later apologised in person.
Revelations by Pakistan-born Rafiq of institutional racism triggered wholesale changes at the club.
Ireland won the toss and opted to field, with both teams showing one change from Thursday.
Innocent Kaia came in for Ballance and the tourists replaced Barry McCarthy with Graham Hume.
Teams
Zimbabwe
Tadiwanashe Marumani, Innocent Kaia, Craig Ervine (capt), Wessly Madhevere, Sean Williams, Ryan Burl, Clive Madande (wkt), Brad Evans, Wellington Masakadza, Richard Ngarava, Tendai Chatara
Ireland
Andy Balbirnie (capt), Ross Adair, Stephen Doheny (wkt), Harry Tector, Curtis Campher, George Dockrell, Tyrone Kane, Gareth Delany, Fionn Hand, Mark Adair, Graham Hume
Umpires: Iknow Chabi, Christopher Phiri (both ZIM)
TV umpire: Langton Rusere (ZIM)
Match referee: Andy Pycroft (ZIM)
