Winning at Wembley with Oldham was a sixth promotion for the 55-year-old Scot, who has managed five EFL clubs.
After guiding the Latics to fifth in the league, Mellon’s team stormed through the play-offs, convincingly beating Halifax Town and York City before winning a thrilling final with the Shrimpers.
And they have shown growing confidence in the higher division – they are on a current unbeaten run of six wins and two draws, which has offered them an outside chance of another play-off campaign.
“Micky’s leadership has helped reconnect the club with its identity and instilled a belief that continues to drive standards higher every day,” said the club’s board.
“His new contract is not only recognition of past success but also a reflection of our shared ambition for the future.”
The Latics’ next game is at home to Harrogate Town on Saturday (15:00 GMT).