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Bournemouth, who were top at the start of the day, could only draw 0-0 at Tranmere but were promoted to the Championship as runners-up.
At the other end, Scunthorpe had their relegation to the fourth tier confirmed after Colchester defeated Carlisle, rendering the Iron's 3-1 win over Swindon futile.
It was a frantic finish for Scunthorpe with all four goals scored in the last seven minutes, including two in stoppage time, but it proved not to be enough.
Swindon took the lead in the 83rd minute through James Collins but Scunthorpe levelled four minutes later through Michael Collins.
Portsmouth, meanwhile, finished their season with a 3-2 defeat by Shrewsbury.
Connor Goldson, Joe Jacobson and Akwasi Asante gave Shrewsbury a 3-0 lead before Ashley Harris and Patrick Agyemang scored for Pompey, but it was not enough to finish their disappointing campaign with a final victory.
A late goal at Elland Road saw 10-man Brighton beat nine-man Leeds to secure a play-off place for Gus Poyet's side in an ill-tempered match.
Will Buckley opened the scoring for Brighton in the 10th minute, with Leeds midfielder Rodolph Austin shown red shortly after.
Brighton's Inigo Calderon was sent off midway through the second half for a challenge on El-Hadji Diouf, who scored the resulting penalty before being sent off himself after appearing to abuse the away fans following the goal.
Jose Ulloa had the final word as he headed a late winner for Brighton.
BLUE SQUARE BET PREMIER
Relegated: Telford, Ebbsfleet, Barrow, Stockport.
Relegated: Bristol City.
NPOWER LEAGUE ONE
Relegated: Scunthorpe, Bury, Hartlepool, Portsmouth.
NPOWER LEAGUE TWO
Promoted: Rotherham, Port Vale.
Relegated: Barnet, Aldershot.