The Blues moved to 26 points, one behind fourth-placed Wellington Hurricanes, with the victory as Beauden Barrett (31) marked his 150th Super Rugby appearance with six conversions and Ricky Riccitelli (28) and Zarn Sullivan (22) each scored a pair of tries.
Waikato Chiefs kept up their 100% record and consolidated top place in the standings as they also scored a bonus point in a bruising 50-17 win over Fijian Drua on Friday.
Chiefs are now on 36 points, five above ACT Brumbies who had a bye at the weekend.
Reigning champions Canterbury Crusaders are third on 28 points after surviving a scare at the Melbourne Rebels and coming from behind to win 43-27 on Friday.
Auckland took a 13-point lead early on before the Waratahs, without 12 regular players who were either injured or resting, went over for their first try.
But scorer Mahe Vailanu (26) was sin-binned soon after and with the one man advantage the Blues were 20-7 ahead at half time and then ran rampant in a rain-drenched second period.
RUGBY GENIUS
Barrett might not have scored a try but his superb tip pass for Sullivan to score was a reminder of his ability to produce moments of rugby genius.
Later on Saturday, there was an upset win for Western Force who overcame the Otago Highlanders 30-17 in Perth with fly-half Bryce Hegarty (30) contributing 18 points.
Chiefs opened the weekend programme with a battling win over the Fijians amid heavy rain in Hamilton, scoring eight tries to three including five in the first half.
But Fijian Drua’s defence improved after the break and the final score was given a flattering boost by three late home tries.
The Rebels were in line for a first win over Crusaders in eight years, leading with 10 minutes left, but replacement hooker Ioane Moananu broke the home resolve with a 70th minute try to turn the result in favour of the champions.
Moananu had been a late call-up for injured All Black Codie Taylor (32).
"He flew over a day later (than the rest of the team) so he was here just before the captain's run. Look he nailed it, didn't he? Just his footwork and his power.
"He's like a little Sevu Reece in the forward pack for us," said Crusaders coach Scott Robertson referring to their injured All Blacks wing.
