Burnett, formerly first-team coach at Victoria Road, was handed the reins in late February after John Still opted to swap the Daggers for non-league Luton, ending his nine-year tenure with the club 16th in League Two and eight points off the drop zone.
Burnett recorded two wins, four draws and six defeats in his 12 games at the helm, narrowly avoiding relegation from the Football League on goal difference despite last Saturday's final-day 1-0 loss at home to York.
The 41-year-old, who has previous experience in charge of non-league Fisher Athletic and Grays Athletic, had stressed his desire to land the job on a permanent basis and was keen to hold talks with the club's powers that be this week.
Those negotiations have on Thursday led to his full-time appointment until 2015.
Chairman Dave Andrews told Dagenham's official website: "I am really excited about the appointment of Wayne Burnett.
"The board of directors were fully committed to offering Wayne a two-year contract despite the mixed results since he took over in February. I feel that now Wayne can prepare for the new season and stamp his own mark fully on the team. We can now look forward to a bright start to a new season."
Burnett enjoyed a playing career which included Premier League football with Blackburn and Bolton as well as spells with Plymouth, Huddersfield and Grimsby.
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