Bernard Parker grabbed a late goal but it proved to be a consolation for Gordon Igesund's men, who failed to qualify for the FIFA World Cup on Saturday.
Igesund, whose position remains unclear after missing out on the World Cup, made 10 changes for the clash against Ian Gorowa's men, who finished bottom of their qualification group without a win.
South Africa had lost just once in six games going into Tuesday's friendly but Zimbabwe started the brighter, with Musona spurning an early opportunity after just two minutes - firing over from close-range.
Musona's strike-partner Khama Billiat was the next to threaten, firing just wide of the post after 20 minutes.
Parker had the hosts' best chance of the half, finding himself free on goal 35 minutes in, before he was dispossessed by a last-ditch tackle to ensure the sides went in goalless at the break.
The visitors took a lead courtesy of a superb Musona effort six minutes after the interval.
The Kaizer Chiefs forward controlled a corner with his chest before firing past Darren Keet in the South Africa goal.
Fans in the Orlando Stadium had to wait until the 94th minute for another goal when Malajila tapped home from inside the area.
Parker grabbed a goal back two minutes later but it was not enough, as Igesund's men suffered a second dose of disappointment in three days.
