Southend left it late - with an injury time goal in extra-time forcing penalties after Wycombe looked to have sealed a famous win.
Phil Brown's side can thank goalkeeper Daniel Bentley who was his side's hero. With Southend 7-6 up in the shootout, Bentley kept out Sam Wood's effort to earn his side promotion to League One.
Earlier, Bentley had deflected Joe Jacobson's 25-yard free-kick into his own net to give Wycombe an extra-time lead.
But Joe Pigott slotted home in the 122nd minute to take it to penalties.
Wycombe goalkeeper Alex Lynch saved the second Southend penalty from Ben Coker but, after Wanderers midfielder Matt Bloomfield - a first-minute substitute for the injured Sam Saunders - missed Wycombe's fourth penalty and the next two were scored, it went to sudden death.
Both sides converted their next two and, after Cian Bolger fired in the 15th penalty of the shootout, Bentley tipped Wood's effort onto the post to end the Shrimpers' five-year stay in the fourth tier.
Defeat will be bitterly disappointing for Gareth Ainsworth's Chairboys, who last season avoided relegation out of the Football League thanks to a final-day win over Torquay.
They finished fourth in the regular season, one place above Southend, and reached the final thanks to a 5-3 aggregate victory over Plymouth.
Preston face Swindon un Sunday's League 1 play-off final and the Championship game sees Norwich face Middlesbrough on Monday.