Premiership favourites headed into the round, Melbourne are now facing the prospect of losing the reigning Dally M Medallist for their title charge.
With Hughes off the field and Cameron Munster and Ryan Papenhuyzen both missing, Harry Grant stood up for the Storm as they won one of the games of the season on Thursday night.
The hooker scored once and then set up two second-half tries, taking charge of Melbourne's attack at Allianz Stadium.
But it also appears likely to be extremely costly, with Hughes leaving the field early in the second half after attempting a tackle on James Tedesco with an outstretched arm and hitting the ground hard after.
Melbourne medical staff then struggled to put the joint back in, prompting the 30-year-old to be taken to hospital in an ambulance.
"He'll probably have to go under to get it back in," Storm coach Craig Bellamy said.
"I don't think it's overly good news.
"I think the longer they're out, it's a bigger problem ... it stretches the ligaments and muscles around the joint."
Melbourne have Tyran Wishart as one option at No.7 after he filled in for Munster at five-eighth on Thursday night, with Jonah Pezet the alternative.
The Storm entered Thursday 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.
"Obviously no one wants to lose their halfback. He is a massive part of our footy team without a doubt," Bellamy said.
"It'll take a bit. We probably won't recover completely, he was the Dally M player last year. However long he is out for, we're going to miss him."
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.
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.
"We had our opportunities, it came down to moments," Robinson said.
"It's tough when you lose a half and your system relies on two halves, which is natural.
"We adapted well in yardage and midfield, and we didn't adapt that well in good ball."
Grant, meanwhile, nailed the key moments.
He scored once 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 at 24-16 down, the No.9 provided the two biggest plays of the second half, first putting King through a hole to score his second.
And with the game on the line and Melbourne down 30-28, Grant made use of a quick play-the-ball, scurried centrefield and sent Stefano Utoikamanu over.
