The Phoenix were well short of being full strength though, despite Ali Abbas starting, with all three goals being scored in the first half.
Midfielder Alex Rufer put Wellington in front with a sharp strike from the edge of the box.
Blacktown struck back when striker Joey Gibbs volleyed the ball into the net after a goal-mouth scramble.
The winner came from the penalty spot in the 40th minute after defender Ryan Lowry was deemed to have fouled an opponent.
Gibbs made no mistake from 12 yards for his second goal of the game.
Phoenix coach Darije Kalezic made changes in the second half, including the 70th minute introduction of Serbian striker Andrija Kaludjerovic for his club debut.
The remaining matches of Wellington's New South Wales tour are against A-League rivals, including Central Coast in Lisarow on Tuesday and Newcastle in Cessnock four days later.
The A-League season commences on Friday, October 6.