In a slightly surprising move, Phoenix coach Ernie Merrick dropped regular left back Manny Muscat in favour of Louis Fenton with Michael Boxall on the right.
The positional switch was likely done with attacking intent as Merrick likes his fullbacks to get forward and provide an outlet but Fenton's defensive frailties were exposed in the 11th minute as the Mariners scored the opening goal through Nick Fitzgerald.
It was Fenton who played the striker onside and Fitzgerald made no mistake as he went one-on-one with Phoenix goalkeeper Glen Moss.
The Mariners enjoyed a greater share of possession during the opening spell and they bagged their second goal via Eddy Bosnar when the centre back smashed home a free kick.
It was sloppy defending from the Phoenix who set up their wall poorly, which left Moss stranded as the home side went to the halftime break in need of a spark.
It came through midfielder Roly Bonevacia when his left-foot shot found the back of the net, which marked their first goal in four games.
That effort kicked the Phoenix in to life and Cunningham, who has been used sparingly this season, was able to make the difference for his team.
His second goal - the winner - came deep in to injury time and it was nearly the last kick of the ball, which banked three points for Wellington.
The result means the Phoenix are still in with a chance of finishing inside the top two on the A-League ladder, which would give them a better road in the playoffs.
While it looks rosy in the short-term, there's still a collection of results in play this weekend that will further shape the standings.
Wellington finish the regular season with a home outing against Sydney FC next Sunday, which is a game that could have implications on who will finish where.
Wellington Phoenix 3 (Roly Bonevacia 65, Kenny Cunningham 79, 90+5)
Central Coast Mariners 2 (Nick Fitzgerald 11, Eddy Bosnar 35)
HT: 0-2
