At 2-2 in the 97th minute in Gosford, homecoming hero Andrew Redmayne made a match-saving penalty save to deny Eli Adams, then the Mariners went down the other end and Nicholas Duarte scored the winner in the 98th.
Sunday's derby victory capped an emotionally draining two weeks for the Mariners, who have ownership speculation hanging over the club, and was a memorable first game for interim boss Warren Moon.
The Mariners were shellshocked when treble-winning coach Mark Jackson quit on October 10 to take up a role at Thai club Buriram United.
It meant the Mariners entered Sunday's season opener against newly crowned Australia Cup champions Newcastle as underdogs - then came out of a rollercoaster 100 minutes on top.
"The A-League's back," Redmayne, famous for his penalty shootout heroics with the Socceroos against Peru, told Paramount Plus.
"I think we'll surprise a few teams this year.
"We've been written off, but we've got, youthful energy in bucket loads and I think a lot of teams have to watch out for us.
"We're a pretty tight-knit group, and I think this will just galvanise us more."
Goal scorer Duerte, 21, added: "It's beautiful, it's amazing, it's what dreams are made of.
"Everyone's saying that it's a turbulent week. We all miss our coach, Jacko. Huge loss for us, especially this close.
"But this group is special. We're going to do special things this year."
Moon, who confirmed he wanted the full-time role, hailed the Mariners' "togetherness".
The Jets looked on track after young gun Alex Badolato delivered the perfect start in the 14th minute,
Redmayne had just cleared the ball but Badolato collected it and fizzed a wonderful half-volley home.
The Mariners hit back when Lucas Mauragis was brought down by Max Burgess.
Alfie McCalmont expertly dispatched the penalty in the 28th minute and two minutes later, Miguel Di Pizio coolly dragged a long-range shot into the bottom corner to deliver a 2-1 lead.
Newcastle equalised in the 81st minute when Lachie Rose tapped home.
Redmayne tipped a fierce strike from Joel Bertolissio over the bar in the 89th minute.
Christian Theoharous blasted a shot over the bar in injury time, then gave away a penalty on Jets skipper Thomas Aquilina.
But Redmayne batted away Adams' penalty then took a quick goal kick as the Mariners launched downfield.
Central Coast players forced the ball forward and Duarte ran onto it, scored and celebrated with the home fans.
"We went and tried to win the game - away from home as well," Jets coach Mark Milligan said.
"We showed good intent. Obviously disappointing the way it ended.
"It's a tough one to take."
The Mariners next play Sydney away on Saturday while Newcastle host Victory on Friday.
