Floating bone fragments were causing the 23-year-old continual pain and he has made only two substitute appearances in the last two months.
Out: Davies (left) has undergone surgery to cure a long-standing ankle problem
Davies is the third Bolton player to be ruled out for the season in recent months after Stuart Holden (knee) and Sam Ricketts (achilles), but boss Owen Coyle is optimistic the midfielder will be fully fit again by the start of pre-season training.
The Scot said: 'We tried some steroid injections but they've not worked so I felt it was important we addressed it now and it wasn't carrying on into the close season. By doing that we'll have him fit and available for the start of pre-season.
'He's an integral part of what we're doing and it's been a huge blow to have himself and Stuart Holden getting injured at the same time because they're both key players in the engine room in midfield and were a big part of the success we'd been having.'
?Galatasaray in talks to take out-of-contract Elmander away from BoltonIt doesn't get bigger than Bolton! Southern eyes Blackpool win to surviveGive me more! Bolton boss Coyle demands more from super-sub KlasnicBolton Wanderers FC news, features and opinion
?Explore more:People: Owen Coyle
Source: Daily Mail
Source: Daily Mail