Having scored just two goals in his A-League Men's career, former Wanderers defender Mark Natta was in the right place at the right time at McDonald Jones Stadium on Saturday, poking the ball past goalkeeper Lawrence Thomas in the 77th minute to secure victory.
The goal put Newcastle five points clear of second-placed Auckland FC, who play Perth Glory on Sunday.
A busy Eli Adams scored a tap-in from a similar position in the 47th minute to help extend Newcastle's record unbeaten streak to 10 games, after their eight-match winning streak ended last Saturday in a 0-0 draw with rivals Central Coast.
"The biggest question I asked of the players after last week was about our performance, (not being) at the level that they set," Milligan said.
"Why I'm so happy with the performance (today) and feel like it was one of the most complete performances is because at no point did we go away."
It was far from smooth sailing for the Jets, as in-form Bulgarian Bozhidar Kraev celebrated his 100th ALM match with the opening goal for the Wanderers in the 20th minute.
A win would have catapulted the Wanderers into the finals conversation with six rounds remaining as they entered the game following a 4-0 win against Macarthur FC.
But instead, the Wanderers stay at the bottom of the ladder, six points behind the sixth-placed Mariners.
"They (Newcastle) are well and truly in the mix (to win the title). They're not leading the comp by mistake," Wanderers coach Gary van Egmond said.
"From our perspective, we can take a lot of things from what they're doing, to try to better ourselves ... We've still got lots of work to do."
Kraev drew first blood when he headed in a superb cross from Ryan Fraser, but Adams found an equaliser when he poked the ball past the keeper.
Newcastle were again rewarded for their persistent attack when Natta scored in the bottom right corner after the ball clattered through a bunch of players from a free kick.
A desperate Wanderers pushed for a goal in the dying minutes, but James Delianov's safe hands cruelled their chances.
