With the game seemingly heading for a draw, the Bafana Bafana playmaker stepped up and showed great technique to hand his side the three points.
Siyabonga Nomvete threatened from the off with a shot just outside the box, but it was well handled by Washington Arubi.
The Birds were playing some great one-touch silky football but their defence was left breathing a sigh of relief when Buhle Mkhwanazi directed his header narrowly off target.
On the half hour, Mbekile showed why he is highly rated by Steve Barker when he pulled off a crucial interception to steal the ball away from Thabo Mosadi’s feet on the edge of the box.
Swallows came out flying after the restart and felt aggrieved when they were not awarded a penalty when Obadiah Tarumbwa blocked Nomvete’s cross into the box.
Mpho Maruping tried his luck from range a minute later, before Dipsy Selolwane saw his strike brilliantly blocked by Larry Cohen.
Chabangu claim close with a free-kick on 72 minutes, before Greg Etafia pulled off a crucial double save to deny Lucky Mathosi’s header and then Selolwane’s follow-up shot.
At the other end, Arubi made a double save off Lefa Tsutsulupa’s header and then a near post tap-in to keep the scoreline goalless with just eight minutes to go.
However, Chabanga had the final say when he produced an audacious goal in which he lobbed a shot over Arubi and into the back of the net with just a minute to go.