Moloney had scans on his shoulder on Tuesday and it was found that there was significant damage.
He is now likely to have surgery, which will all but end his year, with a decision to be announced when he meets with the specialist later this week.
Melbourne football operations manager Ross Monaghan said it was an unfortunate situation for the in-form ball-winner.
"There is a significant amount of damage to his shoulder and the most likely outcome is that he'll have surgery, which will obviously mean he won't play for the rest of the season," Monaghan said. "That's to be confirmed, but it's the most likely outcome.
"That's a real blow to him because he's been starting to hit some form and he's been really positive and he's shown some real responsibility around the place and he's been going really well, so it is disappointing."
Meanwhile, defender Jared Rivers strained abdominal muscles against the Pies.
He will require further testing over the next week and will miss this Sunday's clash against Richmond at Telstra Dome.
Monaghan highlighted that Rivers fell awkwardly on the weekend.
"Things are still a little bit sketchy with Riv … we're not exactly sure where he's up to, but it appears he's strained part of his abdominal muscles and areas around his groin," Monaghan said.
"He's probably done it in one particular action and landed really awkwardly on the weekend.
"It was a really sudden thing that really came on, but it was one particular moment where he landed awkwardly and his back really arched and he really strained himself and from there he couldn't run.
"Until that settles down, we're not exactly sure how long [he will be sidelined] but he won't play this weekend."
