Reports suggested Allie had been on the verge of signing with the Students for several weeks as details were sorted out between the clubs and player.
The move was confirmed on Wednesday by an official statement from The Clever Boys, which read: "Bidvest Wits is pleased to announce the signing of Nazeer Allie from Ajax Cape Town. The 30-year-old defender is an accomplished footballer and brings to the squad a wealth of experience."
This will only be the second club Allie has played for as a professional after spending his entire career so far with the Urban Warriors.
Allie made 27 appearances for the Cape side last season as they finished fifth in the Premiership and were runners-up in the Nedbank Cup after losing to Mamelodi Sundowns in the final.