Wycombe and Exeter were promoted from Coca-Cola League Two as Bury were forced to settle for a place in the play-offs in a dramatic finale.
Wanderers needed only a point at home to Notts County to guarantee a top-three finish but they slumped to a 2-1 defeat.
John Thompson put County ahead (30) and then scored the winner in the 90th minute after captain David McCracken (52) had equalised for Wycombe.
Richard Logan's 71st-minute goal gave Exeter a 1-0 win at Rotherham to ensure they clinched second place. It could have been better for the Grecians but Stuart Fleetwood missed a penalty after Dale Tonge was sent off.
Bury knew only a win would give them any chance of automatic promotion and they snatched the three points in injury time thanks to Phil Jevons' penalty after Andy Procter was sent off. Peter Cavanagh had earlier missed a spot-kick for Stanley.
That 1-0 victory put the Shakers on the same points as Wycombe but they missed out by one goal courtesy of the Chairboys' better goal difference.
Shrewsbury clinched the final play-off place with a 2-1 victory at Dagenham and Redbridge to leapfrog their opponents into seventh.
Grant Holt (19) and Chris Humphrey (33) put the Shrews two up, Paul Benson pulled one back eight minutes into the second half but they could not force the draw they needed.
Chester's relegation was confirmed by their 2-1 defeat against Darlington. Pawel Abbott (71, 90) scored twice for the Quakers either side of an own goal from Ian Miller (89).
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