The squad paraded down Victoria Avenue in Southend at lunchtime before turning into London Road.
The honour came after the squad won 7-6 on penalties against Wycombe Wanderers.
Blues' club boss Phil Brown said it had been "a phenomenal season" and the team had shown "their never-say-die attitude again".
He added: "The last time I was at Wembley in a play-off final was with Hull City. Winning that day was special, but this feels even better.
"The young lads and the old lads did themselves proud."
Southend United are holding an open-top bus parade to celebrate promotion to League One after the play-off final at Wembley.