Stephen Humphrys’ late goal saw Southend beat Sunderland to retain their League One status, while Luton secured the title with victory over Oxford.
The Shrimpers looked to be heading down before Humphrys struck with just three minutes left to seal a 2-1 win.
John White had put the home side in front at Roots Hall from a corner just before half-time, but Chris Maguire equalised with a penalty in the 75th minute.
Luton, meanwhile, made sure of the championship trophy ahead of Barnsley, who lost 2-1 at Bristol Rovers.
Southend’s late show sent Plymouth down, despite the Pilgrims beating fellow relegation batters Scunthorpe 3-2.
Walsall’s goalless draw at Shrewsbury was not enough to prevent them from dropping into League Two.
AFC Wimbledon, though, survived after a 0-0 draw away to bottom club Bradford.
At the other end of the table, Doncaster made sure of their play-off place with a 2-0 win over Coventry.
Peterborough beat Burton 3-1, but finished in seventh place – just a point behind Rovers.
Charlton go into the play-offs having ended the season in third following a 4-0 home win over Rotherham, with Joe Aribo, Lyle Taylor and Krystian Bielik all on the scoresheet at The Valley.
Portsmouth are fourth after a 1-1 draw against Accrington, while Sunderland’s defeat sees them confirmed in fifth place.
The Hatters had already secured promotion, and two goals from George Moncur helped see of Oxford at Kenilworth Road.
Elliot Lee was also on target for the home side early in the second half, while defender Luke Garbutt had pulled a goal back for the U’s on the hour before Moncur wrapped up the title.
At Home Park, it had looked as if Plymouth were going to pull off the great escape as Lloyd Jones and Freddie Ladapo put the home side seemingly in control.
Kyle Wootton pulled a goal back before the break and Josh Morris equalised on the hour, after Pilgrims keeper Matt Macey had tried to throw the ball out to get treatment.
Graham Carey restored Argyle’s lead, but events on the Essex coast took fate out of their hands, with relegation confirmed on goal difference.
Joe Jacobson scored direct from a corner to give Wycombe a 1-0 win over Fleetwood, which saw the Chairboys pull clear of the survival battle.
Doncaster made sure of their play-off place after headed goals in each half against Coventry from Kieran Sadlier and John Marquis.
Ivan Toney had scored twice for Peterborough in their 3-1 win over Burton, but it was not enough to sneak into the top six.
Portsmouth had to come from behind after Sean McConville put Accrington ahead soon after the restart, with Ben Close equalising on the hour.
Barnsley had already been sure of automatic promotion following midweek results, but could not end the season with victory at the Memorial Stadium.
Kieffer Moore had put the Tykes ahead in the 12th minute but defender Liam Lindsay was sent off for a second caution just before half-time.
Alex Rodman’s deflected shot drew Rovers level after 71 minutes before the winger snatched all three points in stoppage time.
Elsewhere, Tom Eaves scored twice in the first half as managerless Gillingham won 3-0 at Blackpool.
Stay updated with the latest news, gossip and football stories by following us @Football_P