Diyo Sibisi handed Ea Lla Koto a second half lead before Patrick Apataki equalized.
However, the Brazilians were dealt a harsh blow in the first half of the match when winger Dillon Sheppard was rushed to hospital with a broken leg following a challenge by James Matola.
Mbulelo Mabizela was also omitted from the Sundowns squad just before kick-off after sustaining a hamstring injury during the warm-up.
Free State Stars started the game well, with skipper Duncan Lechesa forcing Brian Baloyi into a good save in the third minute of the match.
Baloyi was called into action two minutes later when he saved a header by Diyo Sibisi, and the Brazilians then immediately launched an attack of their own, which culminated in Lerato Chabangu shooting wide from the edge of the area.
Sundowns was forced into their first substitution in the 20th minute when Brent Carelse replaced Sheppard, who was caught on the shin by Matola’s knee as he attempted to shoot.
Apataki almost put Sundowns ahead in the 36th minute when he rose highest to latch onto a Carelse cross, but the striker’s header flew straight at Kennedy Mweene.
The match remained goalless at half-time.
Ndlovu should have put Sundowns ahead in the 57th minute when he ran onto a good pass by Chabangu, but the Zimbabwean sent his shot woefully wide of goal.
Free State Stars took the lead in the 63rd minute when Baloyi could only parry Fanyana Dhladhla’s shot, with Sibisi slotting home at the far post.
But their joy was short-lived as Gordon Igesund’s men drew level seven minutes later when Apataki slotted home from Josta Dladla’s free-kick.
Sundowns thought they had taken the lead in the 77th minute when Kampamba Chintu steered Carelse’s shot into his own net, but Esrom Nyandoro, who was lurking behind Chintu was adjudged to have strayed into an offside position, and the goal was disallowed.
The match ended 1-1 after the regulation 90 minutes and forced into extra-time.
Stars threatened first in the fifth minute of extra-time when Thulasizwe Mbuyane forced Baloyi into a good save from long-range, and two minutes later Mbuyiselo Sambu hit the crossbar from range, with Baloyi well beaten.
Sundowns took the lead five minutes later when Ndlovu found himself on the end of a flowing move, in which Chabangu was prominent, and the striker made no mistake, blasting the ball past Mweene.
Referee Ace Ncobo turned down Free State Stars’ penalty appeals in the second minute of the second half of extra-time, when Oscar Ntwagae handled the ball inside his area.
Ea Lla Koto had one final chance of drawing level when substitute Sfiso Sithole weaved his way into the Sundowns area before forcing Baloyi into parrying his shot, but Sibisi was unable to dispatch the loose ball into the back of the net.