The 19-year-old St Kilda midfielder had the arthroscopic stabilisation of his right shoulder earlier in the week.
Dunstan has managed 16 games in his debut season and has made a big impact after starting in the centre-square in his first AFL appearance.
"Luke had routine surgery this week following some relative limitations with his shoulder in recent matches," head of football Chris Pelchen told the St Kilda's website.
"He has had an outstanding debut season with the Saints and we look forward to him starting pre-season training with the other players in November."
Only this week, Hayes indicated he would like to see Dunstan take on his No.7 guernsey – also worn by Nicky Winmar – next year.
Hayes has mentored Dunstan since his arrival at the club and is a big supporter of the young South Australian.
"That's something we'll talk about over the next few weeks," Hayes told Fox Footy's On The Couch on Monday night.
"But he's certainly a guy I've worked really closely with and I love the way he goes about it.
"So I could see him fitting very nicely into it (the No.7 guernsey). But we're yet to make a decision on that."
Dunstan remains in contention for the NAB AFL Rising Star award after being nominated for his 21 possessions against Melbourne in round one.
He stood up in the Saints' win that day, which came despite a depleted midfield that was without Leigh Montagna, Jack Steven and Hayes.
Dunstan has slotted into senior football so smoothly - he's ranked equal fifth at the club for disposals behind Hayes, Montagna, Farren Ray and Jack Newnes.
He's also ranked fourth in contested possessions, third in handballs, sixth in tackles and fifth in clearances.
In better news, defender Jarryn Geary looks set to be available for the Saints' round 21 clash with the Sydney Swans next Saturday.
Geary ruptured a ligament in his elbow in round seven against Hawthorn.
