From that seventh corner, City worked their way downfield and found ever-dangerous striker Manel Exposito. He played the ball harmlessly forward but in racing back to clear, Ross McKenzie succeeded only in diverting away from goalkeeper Danny Robinson and into his own goal.
The second such blunder came when Daniel Koprivcic fired a shot which Waitakere central defender Tim Myers, in trying to block, deflected away from Robinson and watched in horror as he too found his own goal.
After just three rounds, six own goals share the golden boot lead with Canterbury's George Slefendorfas.
By the end of the half McKenzie had atoned for his earlier blunder when he floated in Waitakere's 10th corner and beat City goalkeeper Jacob Spoonley's attempt to keep it out.
The unusual goal-scoring trend continued after the break when, in a seemingly harmless situation, the ball was passed back to Robinson who instinctively picked it up and handed City an attacking indirect freekick.
David Mulligan touched the ball to Exposito who tapped it back and Mulligan unleashed a thunderbolt into the top of Robinson's goal.
Waitakere continued to force corners, 14-2 on the final count, but could not bridge the gap as City ended the day three points clear in continuing their unbeaten start - in all competitions - to the season.
"It was very intense out there," said City head coach Ramon Tribulietx. "I thought there was a foul on our goalkeeper for their goal but otherwise I thought we coped well with the pressure they put us under. We kept playing our style which was important.
"We will take the win. I'm sure we could have scored more if we had been more patient."
Emblen was philosophical.
"After the way we started we looked like we were going to be the team to win today but you can't give a good team like them three goals. To be fair, they defended the attacking opportunities we had well most of the time.
"We went a bit flat when we conceded that third goal but overall, I think they have been tested again by us. Good luck to them in Japan. I'm sure we will meet again this season."
Hawkes Bay United surprised Canterbury United with 3-0 at Park Island for their first win of the season while Otago United came back from 0-2 at halftime to beat YoungHeart Manawatu 3-2 to also score their first victory.
Team Wellington bounced back to beat Waikato FC 3-0.