Midfielder Davies played and scored in the 2-2 draw with Huddersfield on Saturday but sustained a shoulder injury after falling awkwardly.
Although Davies completed the full 90 minutes, Wanderers confirmed via their Twitter account that the ex-Wolves man had undergone surgery on the injury and is set to miss up to three months.
Former Leicester defender Mills also picked up his injury against the Terriers, coming off five minutes prior to the end with a thigh injury.
Dougie Freedman's side are now likely to be without the defender for up to six weeks.
On Davies, who has appeared in all but one of Bolton's league games this term, Freedman told the club's official website: "Unfortunately we'll lose Mark for a period of time. He's cracked his shoulder and unfortunately in football these kind of incidents occur.
"Mark loves his football and was desperate to stay on at Huddersfield. Unfortunately he was in some discomfort on Monday morning and the scan confirmed the news."
It is a big blow to Wanderers, currently 18th in the Championship table, as they prepare for a congested festive fixture list in which they face three teams below them before the end of December.