That late winner, which came after the Phoenix defence fell asleep at exactly the wrong time, only added to a frustrating opening three games for Merrick. Wellington are marooned on the bottom of the table and already nine points behind tonight's opposition but, with that ghastly equation out of the way, there were actually reasons for the coach to be encouraged by what his charges produced against Sydney.
Playing with a full-strength, well-rested squad for the first time, the home side were for large stretches the better team at the Cake Tin, with a seemingly potent attacking lineup on paper at last translating to the pitch.
Sydney might have come into the clash boasting consecutive convincing victories but, before the goal, Glen Moss was rarely threatened, producing one super save in the first half while watching his teammates pose most of the menace.
Krishna in particular proved elusive down the left, sparking the game to life with two early raids and stinging the gloves of Danny Vukovic on another couple of occasions. The Fijian regularly found space behind the Sydney defence and one such instance saw the flag raised moments before he had rounded the keeper and rolled into an empty net, with replays showing the officials had erred.
That call only added to Wellington's sense of persecution, considering Michael McGlinchey had seen an earlier effort correctly waved off, and it certainly spoiled a strong first half.
With more than 60 per cent possession and with Gui Finkler providing a fluid link between defence and attack, perhaps the only disappointment for the Phoenix was their failure to replicate those efforts in the second spell.
Instead, Sydney gradually gained a greater foothold on the game and, after David Carney spurned a golden chance, the Phoenix were warned. It was, however, a warning they failed to heed.
Wellington Phoenix 0
Sydney FC 1 (M. Ninkovic 90+1)
Halftime: 0-0