If the Phoenix had've beaten Sydney they would have finished second, which would have given them a bye during the first week of the playoffs before hosting a semifinal.
A missed penalty from Roly Bonevacia dented the confidence of the Phoenix last night who then conceded two first-half goals, which proved too much of a deficit to overcome.
Former Phoenix striker Shane Smeltz showed how it was done from the penalty spot when he made no mistake in the 32nd minute and that goal proved decisive.
Right back Michael Boxall, one of Wellington's best, pulled a goal back early in the second spell but they were unable to conjure up any more late theatrics.
"We are playing good football, we've just got to finish it off," Merrick said.
The Phoenix were without goalkeeper Glen Moss who missed the game due to a knee injury but he was expected to return against City. In Moss's absence, Lewis Italiano was given his A-League debut and was generally sound.
Sydney, who finished second on the ladder behind minor premiers Melbourne Victory, completed an unbeaten road campaign for the 2014-2015 season.
"It's about togetherness and it's about keeping the same routine whether we are at home or away," Sydney coach Graham Arnold said of his team's road success.
Sydney will enjoy a bye during the opening round of the playoffs and Arnold said his side would be tough to meet in a knockout game.
"I honestly believe that we are the form team of the competition."
Sydney FC 2 (Bernie Ibini 14, Shane Smeltz 32 pen) Wellington Phoenix 1 (Michael Boxall 46) halftime: 2-0