Pavlich, who led the Dockers to a sixth-place finish last year after a brilliant second half of the season, requires a minor operation on his back.
However, the club's general manager of football operations Chris Bond said the big forward should be ready to line up in the club's NAB Cup campaign.
"At this stage we envisage that it will have little impact on Matthew's pre-season training and expect him to be right to play during the NAB Cup," Bond said.
Thomas is set for a longer lay-off, with news he and team-mate Tyson Goldsack will require surgery on ankle injuries, keeping them out of pre-season training until January.
Thomas suffered an ankle injury during a defeat to Carlton in Round 15, while Goldsack picked up his issue in the Round 19 victory against St Kilda.
Both men played on for the remainder of the campaign, Thomas registering three goals in the semi-final win over West Coast despite carrying the complaint.
Utility Goldsack went under the knife earlier this week, while Thomas' operation will take place on Friday.
"The assessment at the end of the season was that a long spell from playing and training, a break, was going to have them all clear for the start of pre-season training," Collingwood director of football Geoff Walsh said."But they've come back and discovered, through training, that they're still being troubled. So we've decided to have them both operated on ASAP."