Tashreeq Matthews opened the scoring in the eighth minute against the ABC Motsepe side at the Lucas Masterpieces Moripe Stadium.
Matthews was then sent off on 48 minutes, but only after a Bathusi Aubaas had put Downs in control of the tie with his goal on 27 minutes.
Sundowns started on the front foot with Arthur Sales close to an early opener with a shot he flashed just past the poles.
But Downs were soon in the lead when Matthews netted with a back-heel from close range.
Aubaas then found himself well placed to fire home on the volley for a second goal in an eventful first half where Sales was again narrowly wide.
The second half had barely started when Matthews as given his marching orders for a second bookable offence.
Tebogo Mashego tried his luck from range, but his show was easily collected by Home Defenders goalkeeper Buhle Thompson.
Malibongwe Prince Khoza was wide with a headed effort, while the Third Division side tried to make the most of their man advantage after the break and twice rattled the crossbar.
Aubaas also had to be alert with the time winding down as he made a crucial intervention inside his area.
But despite some late pressure from the away team, the Premiership side ultimately ran out comfortable victors.