The third Sundowns goal, scored by Sibusiso Vilakazi on 60 minutes, should have been disallowed as TV replays showed Themba Zwane was offside in the build-up.
Furious AmaZulu supporters in a sell-out 10,000 crowd at King Zwelithini Stadium in Durban reacted by hurling bottles, cans, stones and pieces of bricks at the Sundowns bench.
Sundowns’ reserves and coaches moved on to the pitch for safety, no injuries were reported and play eventually resumed with no further incidents.
AmaZulu coach Cavin Johnson slammed the match officials, saying they ruined what had been a thrilling league match until the controversial goal.
“The decision to award the third goal was totally unacceptable,” he said. “The man in the middle spoilt was had been a great game.”
Sundowns coach Pitso Mosimane dodged questions about the crowd disturbance, preferring to praise his team for stretching their Premiership lead to seven points.
“We have been working hard at training on how to create space and our efforts paid off tonight,” said the 2016 CAF Champions League-winning coach.
“Our work off the ball was great and it was nice to score three times and boost our goal difference.
“We have a seven-point lead, but it is not enough. Should we suffer one loss, our challengers will be back in the race,” warned Mosimane.
Brazilian Ricardo Nascimento gave Sundowns a first half lead that was cancelled before half-time when Mhlengi Cele scored after AmaZulu were awarded an indirect free-kick.
Vilakazi put Sundowns ahead a second time on 49 minutes and then struck again after a Zwane shot came back off the post.
Sundowns have 43 points, Orlando Pirates 36, Kaizer Chiefs 35 and Maritzburg United, Free State Stars and Cape Town City 34 with seven rounds remaining.
Pirates and Chiefs clash Saturday before a probable 90,000 crowd with both clubs desperate to avoid a draw, the most common result in Soweto derbies.
Cape Town City have put Ayanda Patosi on a diet at his expense to shed kilograms and he scored the first goal in a 2-0 home win over mid-table Chippa United.
Goalkeeper Daniel Akpeyi, who hopes to be part of the Nigeria 2018 World Cup squad, was at fault for the second goal, allowing an angled free-kick from Lyle Lakay to beat him.
The result snapped a four-loss Premiership run by Cape Town while Chippa have gone eight matches without a victory.