Williams reunited with his former Coventry City manager Gordon Strachan at Premier League club Southampton on 26 October 2001, signing on a short-term loan with a view to a permanent move. He made his debut the following day as a first half substitute for Claus Lundekvam during a 2–1 defeat to Fulham. After signing on a permanent deal the following week, Williams was a near ever-present during the remainder of the 2001–02 season, making 30 appearances. Injuries disrupted Williams' 2002–03 season, which proved to be a memorable campaign for the Saints, reaching the 2003 FA Cup Final (qualifying for the UEFA Cup) and finishing 8th in the Premier League. Williams' final involvement with the first team was as an unused substitute during the Cup Final, which was lost 1–0 to Arsenal. Williams was released in June 2003, after making 43 appearances during two seasons at St Mary's.