Sundowns shifted focus back to domestic duties after bowing out in the Caf Champions League group stages.
The Brazilians showed their early intentions through a low first-time shot from Silva which sailed off the ground into the hands of Peter Leeuwenburgh after the opening seconds.
Starting with an offensive approach, Sundowns appealed for a penalty after 15 minutes in a coming together between Silva and Kwanda Mngonyama, but Victor Hlungwani dismissed their plea.
The four-match run without a goal for Downs came to an end on 25 minutes when Silva tapped home a rebound for his first for the club after Leeuwenburgh failed to handle Ali Meza’s cross.
A 30-metre run from the centre to the penalty area by Craig Martin almost led to an outstanding goal, but Denis Onyango managed to just tip it away to touch on 32 minutes.
Despite the surge in momentum, City opted to tweak their system with the introduction of Gift Links for Riyaad Norodien on 38 minutes.
Match winner a week ago, Taariq Fielies aimed to continue with the same pedestal after heading from a corner, but the effort went wide on the stroke of halftime.
The Tshwane outfit made their first change straight after the break, as Hlompho Kekana pulled out through a suspected muscle groin and was replaced by Lebohang Maboe.
Looking for a way back, City bombarded the opposing area early on in pursuit of breaking the deadlock but Mngonyama shot over from close range.
Former Sundowns midfielder Teko Modise came close to finding the all-important goal for City, but shot wide from close metres.
Substitute Anthony Laffor used his aerial advantage to good effect after getting on the end of a cross, but failed to head on target on 70 minutes.
With City needing only a goal to get back in the stakes for a spot in the final, the pressure to that appeared to take its toll on the young squad who rushed, huffed and puffed.
A penalty shoot-out loomed large in the closing stages, but Benni McCarthy threw his final dice to prevent that with the introduction of Nana Akosah-Bempah on 83 minutes.
The two substitutes Laffor and Lyle Lakay combined on the edge of the box, with Lakay ending off with a half-volley into Leeuwenburgh.
Minutes later, Silva ran down the byline after beating his marker and pulled a cut back to unleash a powerful shot that Leeuwenburgh spurned back into play.
With the score-line level on aggregate at fulltime, a penalty shootout was needed to decide who would go through to the final.
Akosah-Bempah got proceedings underway with a cool conversion. Meza got Downs up and running sending Leeuwenburgh the wrong way.
This continued the next two kicks, until Silva saw his place-kick saved by Leeuwenburgh, with Matthew Rusike grabbing the advantage for City with a blistering finish.
Fielies then converted their fourth penalty easily, which put pressure on Laffor to do the same but he was denied by Leeuwenburgh to give City the win and a place in the final again.
Sundowns: Onyango, Langerman, Morena, Lebusa, Arendse, Kekana, Mabunda, Sirino, Zwane, Silva, Meza.
Subs: Ngobeni, Laffor, Brockie, Lakay, Vilakazi, Madisha, Maboe.
City: Leeuwenburgh, Mkhize, Seedat, Mnogonyama, Fielies, Modise, Patosi, Norodien, Nodada, Martin. Rusike.
Subs: Stephens, Kouassi, Links, Akosah-Bempah, Cupido, Matsi, Abrahams.