The Iron finish sixth, setting up a play-off semi-final with MK Dons after Roberto Di Matteo's side ended the regular season in third.
Luke Howell's goal five minutes from time at Edgar Street sealed a 1-0 in over already-relegated Hereford United.
Leeds United moved upto fourth, to gain home advantage in the second leg of their play-off semi-final with Milwall, thanks to a 3-0 home win over Northampton Town.
But while the Yorkshire side were celebrating, the Cobblers were left contemplating next season in League Two as Carlisle took advantage to move above them.
Goals from Luciano Becchio, Jermaine Beckford and substitute Robert Snodgrass took Leeds to their 11th successive home win.
Crewe were relegated after a 3-0 home loss to the champions Leicester City. Bruno Berner, Lloyd Dyer and Matty Fryatt netted for the Foxes.
Carlisle United, no strangers to last-minute heroics, climbed out of the relegation zone thanks to a 2-0 home win over Millwall.
Graham Kavanagh and Paul Thirlwell scored the goals, that saw them stay up.
Brighton completed their escape from relegation with a tense 1-0 victory over Stockport County. Their captain Nicky Forster was the hero on his comeback from injury.
Bristol Rovers completed their season with a 4-1 win over Hartlepool United. Pools could have been relegated, but Northampton's loss at Leeds saved them.
Joe Royle ended his second spell in charge at Oldham Athletic with his first win since his return, as the Latics recorded a 2-1 win at Walsall.
It ended a run of four draws and four defeats for Royle. He will now hand over the reins to the watching Dave Penney who quit Darlington on Thursday to take charge at Boundary Park.
The Southend United captain Adam Barrett and substitute Jean Francois-Christophe secured a comfortable 2-0 win over Cheltenham Town.
Colchester United were 2-0 winners at Yeovil Town thanks to goals from Ashley Vincent and Mark Yeates.