The 23-year-old, who also netted in Zimbabwe's 2-1 friendly victory over South Africa, struck a first-half opener, with substitute George Lebese likewise on target at FNB Stadium.
Musona, though, left the field late in the game with a stomach muscle problem, raising doubts that he will be available for Tuesday's trip to Bloemfontein Celtic.
The result lifts the League champions to fifth place on the table with seven points from four games - two points behind leaders SuperSport United, who visit top tier rookies Mpumalanga Black Aces on Sunday.
United are 11th in the standings with four points.
In a lively contest, the hosts threatened 14 minutes in, as Musona forced his way past debutant Robyn Johannes and unleashed a low shot, triggering a fine diving save from Man of the Match Shu-Aib Walters, who reacted sharply to foil Bernard Parker on the follow-up.
Soon after Walters did well to parry away a useful long-range effort from the in-form Parker, who has three League goals this season and netted thrice during the recent international break.
Chiefs' Siphiwe Tshabalala flashed a shot wide midway through the stanza, while his teammate Kingston Nkhatha had a deflected crack on goal collected by Walters just past the half-hour mark.
At the other end, Ruben Cloete thumped a loose ball just over the goal, with Glamour Boys captain and goalkeeper Itumeleng Khune scrambling to cover.
Stuart Baxter's men, however, drew first blood in the 37th minute, as Musona pounced on the rebound after Tshabalala's deflected strike hit the upright.
United showed promise five minutes after the break, as Terrence Mandaza's header required a save from Khune following debutant Ashley Hartog's telling cross from the right.
Musona came close with a swift shot on the turn in the 58th minute but Walters was alert to the danger.
Moments later Cloete had an attempt nicely kept out by Khune, while Rheece Evans headed over from range shortly after.
Musona then curled a shot over before strike partner Nkhatha pulled the trigger with intent, but Walters was once again perfectly positioned to make a crucial block.
Walters, however, was eventually beaten in the 75th minute, as Lebese tapped in from close range barely two minutes after replacing Musona.
The Team of Choice were unable to find a way back in the closing stages.