Former All White Pearce nearly brought the scores level four minutes later when he fired a stinging shot off the underside of the crossbar before it was cleared to safety.
Auckland continued to control the tempo and flow of the match without creating any clear cut chances until Manuel Exposito fired wide late in the first half, when the experienced South American should have done better.
Former Canterbury United striker George Slefendorfas levelled the game inside two minutes of the second half when Auckland goalkeeper Jacob Spoonley ripped a wayward clearance off the back of the Waitakere striker only for the ball to loop into an empty net.
The second half then turned into an open, fiery end-to-end encounter that saw four yellow cards in quick succession, all for late challenges.
Ramon Tribuletix will be disappointed with his side's finishing after Koprivcic, Corrales and Dickenson all squandered good chances to put the game away.
In the end it was the pace of Pearce down the right side which opened up the Auckland defence, before he slid the ball across the six-yard box for Manko to score the easiest of tap-ins.
"It isn't the be all, end all, for us, there wasn't any points up for grabs, but we wanted to win this game and turn the tide. I thought the players did very well today," said Waitakere United coach Paul Marshall.
"That's a result without Ryan de Vries or Roy Krishna, but we have some good players to come in, exciting, quick players. Roy couldn't play but he's a talent, he's special. All the games will be tough, you still have to win, the league is getting closer, getting tighter.
Auckland City are home to Canterbury United on Saturday while Waitakere United open their ASB Premiership defence at home on Sunday to Team Wellington while other two matches on Sunday see YoungHeart Manawatu away to Otago United and Waikato entertain Hawke's Bay United.
