The experienced defender has been handed a new one-year deal, despite his 2017-18 campaign being blighted by injuries.
"It's been a long journey - a lot of hard work, a lot of sweat and a lot of tears, but we're finally there now," Webster told Millwall's official website.
"It's good to be back involved in the banter with the lads. When you're injured, you're involved, but not properly. It's good to be a part of the mix again.
"A lot of credit goes to Paul (Tanner, Millwall's physio) and the medical stuff. It's hard by yourself, but they give you a kick up the backside and motivate you to do more and do it right."