Luis Corrales scored after 16 minutes, with Dominic Rowe and Adam McGeorge netting within six minutes of each other later in the half.
Despite the Bay hitting back quickly through Stephen Hoyle and Dakota Lucas, a Hamish Watson strike almost straight after the second half whistle went, killed off their hopes.
Nevertheless, there was a logic behind the Englishman's thinking as he prepares his team for their first playoff campaign. He opted to rest three key players - captain Bill Robertson, midfielder Conor Tinnion and former All White front man Jarrod Smith. He also tinkered with their style.
"We've changed things, such as having more discipline and aggression all over the park, and changed those things because of next week. Some players have been asked to do things they've not done before," he said.
"I'd rather play Waitakere with a fit side, than face Auckland with six or seven of our key players out. It was far from ideal. I mean, I wanted to play our strongest 11 but that wasn't the case."
Greatholder hauled off Aaron Jones and Stephen Hindmarch, who were both booked for their involvement in a needless skirmish in the second half, to avoid being suspended for the Waitakere clash.
Despite this lacklustre defeat, Greatholder is in no doubt his side can beat minor premiership winners Waitakere.
"We are ready for Waitakere because we've rested key players and we've got our best 11 players for next week. We know what we need to do to get better and I firmly believe we will win the game."
He will, however, have to place more emphasis on defence, especially as his side conceded two "horrendous goals".
Auckland yesterday beat Manawatu 4-1 in Palmerston North for the men in green to finish dead last two seasons in a row while in the battle for the minor spots, Waikato FC downed Otago United 3-1 at Ngaruawahia to finish sixth.