But they played with renewed vigour and purpose against the heavily favoured Roar outfit despite a setback only 19 minutes into the game when Marco Rossi was subbed off with a hamstring injury.
Both sides had their attacking moments in the first half but it was Smeltz who broke the deadlock in the 32nd minute.
Recruited back to the club last month, Smeltz struck with a well-taken header after Adam Parkhouse had cut down the left wing and popped a perfect cross.
Unmarked at the back post, the Phoenix goal-scoring machine made no mistake in neatly tucking the winning goal away.
A surprisingly limp Brisbane tried to fight back in the second spell only for Krishna to break the hearts of local fans.
Krishna coolly netted in the 62nd minute after finishing off a slick movement involving Smeltz and Kosta Barbarouses whose deft touches even drew applause from Roar fans.
Brisbane grabbed a good goal back in the 75th minute through Brandon Borrello to give themselves a fighting chance but could not nail an equaliser.
The visitors were without Roly Bonevacia, Tom Doyle and Ryan Lowry who were all sensationally dropped after what has only been described as "an internal matter that has been dealt with" and a "lack of professionalism" by Phoenix co-coach Des Buckingham.
The shake-up, along with Andrew Durante returning from suspension, seemed to have the desired effect with the Phoenix holding on for what may yet end up being their most vital win of the season so far.
Wellington Phoenix 2 (S Smeltz, R Krishna)
Brisbane Roar 1 (B Borrello)
Halftime: 1-0
