The Phoenix scored against the run of play through Roly Bonevacia, after good work by Kwabena Appiah, to level the game 1-1 at the break.
Fiji striker Vakatalesau missed two golden opportunities within the opening 10 minutes of the second spell before Tom Doyle's superb cross found Phoenix winger Appiah, who shot straight at the keeper.
Moss was again superb with a point blank save from another Krishna thunderbolt before Doyle won it for the Phoenix with a fiercely-hit cross that somehow ended up in the back of the net from an acute angle.
Phoenix coach Ernie Merrick was happy enough with the first hit-out ahead of the second game in Ba on Tuesday.
"I was pretty happy with the defence overall and Glenn Moss was one of our best players," he said. "We had a couple of players playing out of position and when we were attacking we weren't covering at the back and got caught out, so that is something to work on."
In the early game, the Phoenix Premiers went down 2-1 to the Fiji under-23s after leading 1-0 at halftime through 16-year-old captain James McGarry, who played the final 20 minutes of the main game.
Fiji 1 (Roy Krishna 24') Wellington Phoenix 2 (Roly Bonevacia 40', Thomas Doyle 77'). Halftime 1-1.
# Peter White travelled to Fiji courtesy of Fiji Airways.