Awford initially took over on a temporary basis in March 2014 after Richie Barker's tenure and guided the club to safety in the fourth tier last season.
However, Portsmouth have endured an inconsistent campaign, with Saturday's 3-1 defeat at Morecambe leaving them 14th in the table, and the decision has been taken for Awford to step down from his role.
The 42-year-old is a well-respected figure at Fratton Park having played for the club for 11 years and was a part of the team that took Liverpool to an FA Cup semi-final replay in 1992.
Portsmouth have confirmed that further talks are planned to find a different position for Awford, while assistant manager Gary Waddock will take charge of the team for the final four matches of the season.
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