Second-half tries from skipper Cameron Smith and Billy Slater helped an uncharacteristically sluggish Storm side claim the two points to put a dent in the Knights' top-eight aspirations.
However, the game's biggest talking point was the decision not to sin-bin Cooper Cronk in the 55th minute when the Queensland halfback took out Darius Boyd without the ball when he looked set to latch onto a Jarrod Mullen kick 10 metres in front of the Storm's line.
After liaising with the video referee on-field official Jared Maxwell deemed the offence was only worthy of a penalty which Gidley converted.
And to add insult to injury for the hosts, Cronk then set up Slater to score nine minutes later with a pinpoint chip-kick to give his side a lead they never relinquished.
Cronk then iced the game with a field goal seven minutes from time before veteran prop Bryan Norrie dived over in the final minute to give the Storm a comfortable winning cushion.
Newcastle controlled the opening stanza in front of a hostile home crowd of 26,832 but had only two unconverted tries to show for their dominance with Gidley missing from the sidelines after Joey Leilua and Akuila Uate went over.
Smith then handed the ball straight back to the Knights when he kicked out on the full.
But the hosts failed to capitalise and the Storm gave themselves a much-needed four points when giant young back-rower Jordan McLean crashed over on the stroke of halftime.
However, Smith then saw his conversion attempt in front of the posts crash back off the upright.
But after the break the Test skipper showed all his class with a much improved display, diving over from dummy-half following a neat show-and-go, before adding the extra two points.
Uate almost got the Knights back in front midway through the second period, but the winger's foot touched the line, allowing the Storm to regain possession, take control and grind out the win.
MELBOURNE 23 (J McLean B Norrie B Slater C Smith tries C Smith 3 goals C Cronk field goal) bt NEWCASTLE 10 (J Leilua A Uate tries K Gidley goal).
Referees: Jared Maxwell, Brett Suttor.
Crowd: 26,822 at Hunter Stadium.