Rooney has a thigh injury which will keep him out of action for six weeks.
The devastating news comes just a week after it was revealed that key forward Jonny Hayes will miss a similar length of time with a hamstring tear.
27-year-old Rooney wasn't named in the Dons' first team squad for the Scottish Premiership clash against St Johnstone on Saturday.
Young midfielder Craig Storie, who signed a new contract in midweek, also missed out - and with Shay Logan missing through suspension, Aberdeen's shallow squad was stretched to its limits.
Fans are already starting to query the club's lack of transfer activity in January while allowing David Goodwillie to leave the club and failing to recall on-loan striker Lawrence Shankland.
What's for sure is that Aberdeen will struggle to challenge Celtic for the title with two key components of their squad missing.
Image: PA