New Wellington Phoenix coach Ernie Merrick was proud of his players' efforts but disappointed not to get a point from their opening A-League match against the Brisbane Roar on Sunday.

The stoppage-time goal from Ivan Franjic was a cruel blow for Merrick and his team, who had battled hard at Westpac Stadium without key players Andrew Durante, Jeremy Brockie, Leo Bertos, Glen Moss (all on All Whites duty) and Louis Fenton (dislocated shoulder).

Half of the Phoenix's starting XI was on debut and it was revealed after the game that goalkeeper Jacob Spoonley had also struggled with a virus the previous day and couldn't train.

Yet despite all that, a strong first-half performance, sparked by the dominance of new signing Carlos Hernandez, Vince Lia and Manny Muscat in midfield, had the Roar on the back foot.

The pressure eventually brought a goal for striker Stein Huysegems.

But a half-time pep talk from Roar coach Mike Mulvey saw the visitors come out firing.

Besart Berisha, who had missed several chances in the first spell, scored within less than a minute of the restart.

Then gradually the Roar began to wear down the inexperienced and tiring Phoenix youngsters which eventually resulted in the last-gasp winner from Franjic.

"They (Brisbane) couldn't get out their half in the first 10-20 minutes and we should have taken more of an advantage on the score sheet," admitted Merrick.

"In the second half they scored early and they scored in the last minute. But in between we gave as much as we took but we were running out of legs, the youngsters in particular.

"The boys are still learning what it takes to grind out a result because we should have ground out a point today."

Meanwhile, Brisbane skipper Matt Smith says there is still plenty of work to be done ahead of their clash against Sydney on Saturday despite the victory over Wellington.

Smith, returning to the side after hip surgery, praised his side's resilience for coming back from a goal down but warned his side would need to improve against the Sky Blues at Suncorp Stadium.

"There were probably times last season where we would have gone a goal down and dropped our heads," said the defender.

"This season it's great to see already that the boys will keep pushing and pushing. We can take an awful lot from (the match) despite probably not the best performance.

"Our ball speed at times was particularly slow. It gave Wellington the opportunity to cut out an awful lot of passes.

"We'll have learned a lot from that and credit goes to Wellington because they made it very, very difficult for us.

"That's going to be our task this week to correct the things we did wrong (against Wellington) and to put in a better performance next week in our first home game.

"We aim to create a fortress at home this year."