The Queensland side sealed their second victory in Wellington from 10 rounds of the 2013-14 season thanks to a brilliant strike from their versatile utility player
Roar captain Matt Smith was on hand to scramble a loose ball past Glen Moss in the 37th minute to open the scoring, but Carlos Hernandez levelled from the penalty spot early in the second half.
But just when it looked as if the hosts would secure a much-needed point against the high-flying visitors, Ivan Franjic scored a spectacular goal from the edge of the box to sink the home fans for the second time this season.
Despite the result, Ernie Merrick will be pleased to see one of his main signings registering for the first time after nine matches and a composure often not seen under predecessor Ricki Herbert.
The same couldn't be said for Roar manager Mike Mulvey, whose side looked shaky at times against one of the worst defences in the competition. Their one-goal lead at half-time was no sign of the dominance the hosts had enjoyed, but their experience and ability to capitalise on few chances was a lesson Merrick and the Phoenix need to learn quickly.
The Phoenix didn't look like a side who had gone without a win in the opening half. They created a number of chances thanks to Kenny Cunningham's speed on the attack and Stein Huysegems' positioning.
Huysegems was a threat throughout the first half and when a deflected shot fell to Jeremy Brockie, it looked as if the New Zealand international would secure his first goal of the season. Instead he deflected the ball over the goal for one of the misses of the season.
That anger was compounded two minutes later when Smith gave the visitors a precious and unexpected lead. Smith kneed a contentious free kick past a diving Ben Sigmund and Glen Moss to illustrate why they sit atop the A-League ladder.
If Merrick felt nervous ahead of the match about his side's inability to score goals, there were certainly more questions to be asked at half-time.
Instead of having his head down, Cunningham helped get his side back on level terms when he was questionably brought down in the box by defender Jack Hingert. Hernandez stepped up and scored his first Wellington Phoenix goal.
The Phoenix pressed just as the Roar had done after they had scored their first half goal. The confidence that had evaporated at the 37th minute returned as the visitors were forced to defend.
But Franjic struck again to sink the Wellington Phoenix just as he had done in the first round encounter between the two teams.
Riera looked to have given his side a late equaliser only for the ball to be cleared off