Southgate has been in charge at Riverside for three years and presided over the club’s relegation from the Premier League last season.
His dismissal came in the early hours of Wednesday, just hours after their 2-0 home win over Debry.
Boro chairman Steve Gibson said: “This has been the most difficult decision I’ve ever had to make in football.”
“Gareth has given Boro magnificent service as a skipper and, in very difficult circumstances, as manager,” added Gibson.
“However the time is right for change and that change has had to be made.”
