Aliir was marking the ball in the second term of Saturday night's match when van Rooyen steamed through and attempted to spoil but seemingly mistimed it and instead struck the defender high with a swinging arm.
The Port defender hit the ground at Adelaide Oval and didn't move for several seconds and had to be helped off the field by trainers.
Aliir failed his Head Injury Assessment (HIA) test and spent the rest of his 200th AFL game watching from the bench.
On Sunday, the match review officer charged van Rooyen with striking and assessed the incident as careless conduct, high contact and severe impact, which draws a three-match ban.
That would rule van Rooyen out of next week's game against the Western Bulldogs, then Melbourne's first two finals - or an elimination final then round one next year, depending how the Demons finish.
Unless the fifth-placed Demons, who can still make the top four, are able to appeal the suspension, it means bar a stunning finals run, van Rooyen's season would be over.
Van Rooyen, 23, has kicked 42 goals and averaged 4.7 marks in his best season to date.
Elsewhere, Collingwood dynamo Beau McCreery can accept a $3125 fine for his third offence of making careless contact with an umpire, in the second quarter of Saturday night's draw with Hawthorn at the MCG.
