Without Hughes on the field and with Ryan Papenhuyzen or Cameron Munster playing, Harry Grant stood up for the Storm in one of the games of the season.
The hooker scored once and then set up two second-half tries, taking charge of Melbourne's attack in what could prove a vital victory at Allianz Stadium.
But the win came at a significant cost, with Hughes leaving the field early in the second half with a dislocated left shoulder after attempting a tackle on James Tedesco.
Melbourne medical staff then struggled to put the joint back in, with the injury marking the third time Hughes has dislocated it in his career.
He is set for scans, but the Storm are already bracing for a stint without the Dally M Medallist with Jonah Pezet the option to come in.
Melbourne entered the round in third place with two wins over fifth-placed Brisbane, but have a brutal run home in their bid to finish in the top four.
After Parramatta next week, the Storm have Brisbane, Penrith, Canterbury and then the Roosters and Broncos again in the run to the finals.
Thursday night was also costly for the Roosters' finals chances, after playing the majority of the game without halfback Sandon Smith following a first-half head clash.
Trent Robinson's men will finish the round in 10th, but could be as many as four points outside the top eight with a crucial clash against Manly next week.
In a frantic match of attacking highs, the lead changed hands five times.
Sam Walker kicked for four of the Roosters' tries and helped lay on another when Tedesco batted on a pass from the halfback.Â
Daniel Tupou scored for two of those four-pointers, including one from a pinpoint perfect Walker cross-field kick where he outleapt opposite winger Kane Bradley.
But ultimately it was an error from Tupou that cruelled the Tricolours, with the winger bombing a try over the line with them up 30-28.
Walker also had a costly grubberkick go dead when the Roosters lead 24-22. After both Walker and Tupou's errors, the Storm went downfield and scored shortly after.
Grant, meanwhile, nailed the key moments of the match.
He played a role in the Storm's first when he ran from dummy-half, attracted Tedesco in defence and Hughes grubber-kicked for Josh King to score.
Grant scored one himself when he went over in the first half, splitting Smith and Salesi Foketi as the two clashed heads.
Then with Hughes off the field, Grant provided the two biggest plays of the second half.
Trailing 24-16, he first spotted a hole for King to run through for the prop to score from close distance.
And with the game on the line and the Storm 30-28 down, Grant made use of a quick play-the-ball, scurried centrefield and Stefano Utoikamanu over for the match winner.
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