The Chiefs, with five consecutive victories including three bonus-point wins, hold a four-point lead at the top of the standings over the Wellington Hurricanes, who handed a 59-0 thrashing to the Moana Pasifika on Saturday.
Despite their defeat, the Brumbies sit in third while the Auckland Blues moved up to fourth as they bounced back from last week's loss to the Crusaders to win 30-17 over the Western Force on Sunday.
The Chiefs had to work hard on Friday against a Waratahs side who dropped to 1-4 for the season after a try from flyhalf Bryn Gatland and two from winger Emoni Narawa took the visitors across the line.
"Sometimes it's better to win ugly than it is to lose pretty," coach McMillan said.
"Everyone has games like that, and you scrap to the end and you wish that you had played a lot better, but that's the beauty of our game, that there's always things to work on."
The Hurricanes moved up to second as they avenged a shock loss to the Moana last season, when the newly created franchise claimed their first-ever win in Super Rugby competition, with a brutal display at Auckland's Mount Smart Stadium.
Winger Salesi Rayasi grabbed a brace late in the nine-try win for a weakened Hurricanes side that saw coach Jason Holland rest All Blacks Tyrel Lomax, Dane Coles and Jordie Barrett.
"Feeling very proud of the boys, very happy," said captain Ardie Savea. "To come here and keep Moana to zero is something very special for us. We're going to cherish this one."
The Canberra-based Brumbies had not beaten the Crusaders in their last 11 encounters, and not in Christchurch for 23 years, so resting five key Wallabies for the trip looked almost like a concession.
The Crusaders have been struggling with a lengthy injury list but wasted little time in sending winger Leicester Fainga'anuku across the line for the first of his two tries and a home win never looked in doubt.
Melbourne Rebels bounced back from going behind to two early tries to hand the Queensland Reds a 40-34 defeat in a see-sawing clash on Saturday that saw Angelo Smith power over to score the winning try for the hosts 12 minutes from time.
Injury-ravaged Otago Highlanders, meanwhile, brushed aside their issues to thump the Fijian Drua 57-24, with Martin Bogado scoring two tries as Clarke Dermondy's side moved ahead of the Fijians into eighth in the standings.
