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Wellington played their part in a thrilling match with foreign attackers Tomer Hemed and Ulises Davila scoring, but goalkeeper Oliver Sail was just as important, making superb saves just moments before each of his side's goals, as well as producing several other key stops as the Phoenix soaked up considerable City pressure.
However, he could do nothing to stop the eventual winner, Melbourne City substitute Marco Tilio heading home from close range in the 83rd minute to move his side into second place on the table.
There was far greater urgency from Wellington compared to their lethargic last outing against Macarthur, but as befitting a side high on confidence, City asserted their authority early on, dominating possession and making numerous entries into Wellington's penalty area before the constant pressure eventually told in the 17th minute. A left-wing City corner was met by a virtually unopposed Curtis Good who planted a firm header into the net from six yards.
To their credit, the Phoenix responded well, but found it hard to break down a compact, well-organised City defence. Sail made the game's best save after 38 minutes, diving to his right and getting his fingertips to a close-range effort from Florin Berenguer to thwart the Frenchman. Seconds later, Wellington were level with Hemed producing a fine side-footed finish from the tireless David Ball's left-wing cross after good build-up work from Clayton Lewis and Davila.
City went ahead again just before the interval, the competition's leading marksman Jamie Maclaren restoring his side's advantage with a thunderous left-footed strike across Sail at the end of a fast-break manufactured by Australian youngster Connor Metcalfe. It was City's 17th shot on goal in the first half alone.
Phoenix coach Ufuk Talay responded by introducing Ben Waine and Cameron Devlin at half-time, having earlier made one injury-enforced change to his starting side with influential defender Steven Taylor ruled out with a quad strain. He was replaced by Josh Laws, while attacker Jaushua Sotirio was also promoted.
City squandered a golden opportunity to extend their lead early in the second half, but Sail again saved superbly from Craig Noone with a strong right hand after a City fast-break. It was to prove crucial, with Davila producing a sublime long-range, left-footed finish to square the ledger moments later, before Tilio broke Wellington hearts in the closing stages. Louis Fenton had a late chance to steal a point for Wellington, but saw his injury-time header cleared off the line by Good.
The defeat leaves the Phoenix tenth on the A-League ladder, seven points adrift of the playoff spots with 11 regular season matches remaining. They next face the seventh-placed Western United on Sunday evening.
Wellington Phoenix 2 (Hemed 39', Davila 56')
Melbourne City 3 (Good 17', Maclaren 45', Tilio 83')