Sundowns beat Entente Setif in Algeria 11 days ago, but the result was declared "null and void" when the hosts were disqualified after their supporters hurled missiles and invaded the pitch, forcing play to be abandoned.
Eliminated by V Club in the final qualifying round, Sundowns got back into the competition when the Democratic Republic of Congo team were kicked out for fielding an ineligible player.
Making the most of a second chance, Sundowns lead Group A on goals scored from five-time African champions Zamalek of Egypt, who defeated Enyimba in
Nigeria two weekends ago.
Sundowns and Zamalek have three points each while twice African champions Enyimba are pointless having played a game more than their rivals in a three-club race for two semi-finals places.
Colombian Leonardo Castro poked a loose ball into the net close to half-time and Dare Ojo levelled just before the hour with an unstoppable half-volley.
The winner came 12 minutes from time when a corner was pushed sideways, then crossed to central defender Wayne Arendse on the edge of the six-yard box.
Goalkeeper Moses Ocheje scooped the close-range shot away, but the Burundian referee took his cue from an assistant, who indicated that the ball had crossed the line.
Sundowns succeeded at home after a trend of away victories in the group stage this season continued with ASEC Mimosas of Ivory Coast shocking Al Ahly of Egypt 2-1 in Alexandria.
It was the first time the Abidjan outfit -- the 1998 Champions League winners -- triumphed in four mini-league phase visits to Egypt.
ASEC have performed much better away from west Africa this year in the premier African club competition, winning three of four games while claiming only one victory at home.
They were gifted the winning goal 10 minutes from time when experienced goalkeeper Sherif Ekramy fumbled a harmless header and Armand Niamke pounced to score.
Yannick Zakri scored his third goal of this CAF campaign to put ASEC ahead during the first half and former Fiorentina defender Ahmed Hegazy equalised soon after the break.
It was the second successive CAF loss for new Egyptian title-holders and record eight-time African champions Ahly in a group completed by Wydad Casablanca of Morocco and Zesco United of Zambia, who meet late Wednesday.