Richard Henyekane opened the scoring in the 42nd minute before goals from Ryan Chapman and Bryce Moon gave Wits the lead going into the break, but Alje Scut levelled matters in the 58th minute.
Sundowns went into the encounter looking to secure a place in the top eight, while Wits were eager on cementing fourth spot. The Clever Boys achieved their mission, but Sundowns will miss out on MTN8 action next season.
The first clear-cut chance of the game fell to Sibusiso Vilakazi in the 24th minute after he snuck in behind the Brazilians defence, but the Wits captain was unable to find the back of the net with only the keeper to beat.
The game sparked to life five minutes before the break with three goals being scored in quick succession.
First Henyekane, who earned a surprise Bafana Bafana call-up on Friday, took a step towards silencing his critics when he powered towards the Wits goal and slotted the ball into the net.
Downs only lead for two minutes, however, as Chapman pounced on a loose ball inside the area to net his eighth of the season.
Wits then took the lead just before half-time when Moon scored with a neat backheel from close range.
The frantic end to the first 45 resumed in the second. First Wits left-back Sboniso Gumede was given his marching orders for a second bookable offence in the 57th minute.
The Brazilians immediately took advantage of their extra man, levelling matters through Schut a minute later. The Dutch defender got on the end of a cross from Teko Modise to take his goal tally to four for the season.
The Brazilans pushed forward in search of the winner but the Wits defence stood firm, and Sundowns will have to be satisfied with 10th position.