During their past two meetings they had battled to 0-all draws as they did little more than cancel each other out on both occasions.
Chances were limited during the first 45 minutes as Phoenix midfielder Michael McGlinchey hit the crossbar from a free kick, while Glen Moss cleaned up a few shots from City.
Merrick has tinkered with his starting side in recent weeks and has settled on using Louis Fenton in the midfield after he impressed during their round 26 come-from-behind 3-2 win over the Central Coast Mariners.
Fenton spent most of the season at right back but Merrick wanted to find a way to add Michael Boxall in to the mix after he had impressed during the latter stages of the campaign.
But it seemed an odd time of the season to mix and match your preferred starting side and there was a lack of continuity about the Phoenix in the early going, particularly in the middle of the park.
Striker Roy Krishna has also fallen out of favour in recent weeks with Merrick electing to push Roly Bonevacia forward.
Despite having the better of the game after halftime, the Phoenix went behind on the scoreboard when City forward Josh Kennedy latched on to the ball and grabbed a goal from close range in the 61st minute.
The Phoenix had enjoyed their moments earlier but hadn't been able to build enough concerted pressure to find a goal.
Playing from one behind is troublesome enough but the job in front of the Phoenix got even tougher when an own goal from Moss put City 2-0 ahead.
The Phoenix custodian dived to stop a shot but the ball bounced off the post and hit his body as it rebounded in to the net in one of the more unique goals you'd see.
With the scoreboard making for dire reading, Merrick went to his bench and inserted Krishna, Kenny Cunningham and Alex Rodriguez as he went about a miraculous salvage mission.
But there was no late heroics to be had and the side that had led the A-League after round 22 were bounced from the competition with a whimper in the first week of the finals.
Melbourne City 2 (Joshua Kennedy 61, Glen Moss 72 og) Wellington Phoenix 0 halftime: 0-0