Thomas re-injured his right ankle on Saturday when he returned in the VFL for his first match at any level since May.
He has only managed five AFL matches this season and Thomas will now consult with specialists in Melbourne and Sydney.
The club said in a statement that more surgery was one of several possibilities for the 2011 All-Australian.
The Magpies were hopeful that Thomas would come back in time for the finals.
Thomas is also in contract negotiations with the club and becomes a restricted free agent at the end of this season.
"Dale worked incredibly hard to play again this year and everyone was enthused to see him get close," Collingwood football manager Rodney Eade said in a statement.
"He felt strong and confident and to see him brought down again is a reminder of how tough the game can be at times.
"Right now, we know that the rest of 2013 is out.
"He is going to see several specialists over the next week or so and in terms of what, if any, impact there will be on his pre-season we will have to wait and see.
"A clearer picture of what the options are will emerge once he has been examined."
Thomas originally had ankle surgery last November to repair ligament damage he suffered in round 15.
The Magpies also confirmed on Monday night that Jamie Elliott (hamstring) and Ben Sinclair (shoulder) would miss Friday night's MCG match against West Coast.