David Mirfin's 91st-minute header from Gary McSheffrey's punted free-kick sealed a stunning second-half fightback after Lee Molyneux and Peter Murphy had given the home side the perfect start.
Molyneux broke the deadlock with his first league goal since rejoining Stanley after 18 minutes before Murphy's deflected strike made it 2-0 eight minutes before half-time.
Whatever pearls of wisdom that Scunthorpe manager Russ Wilcox delivered during his team talk at the interval clearly did the trick as Sam Winnall - League Two's top scorer - bagged his 16th of the campaign five minutes after the restart.
Hakeem Adelakun hauled the visitors level minutes later and Paddy Murphy was denied by the crossbar before up popped Mirfin in added time as Scunthorpe completed a smash-and-grab raid that puts them on 55 points along with Chesterfield, who lead by virtue of a better goal difference.
Elsewhere in the Football League on Friday, Walsall missed the opportunity to leapfrog Peterborough United into the League One play-off places as the two sides drew 0-0 at London Road.
Swindon Town and 10-man Colchester United also settled for a point of piece in another goalless draw.
Sanchez Watt, the former Arsenal man, was the player to be given his marching orders following an altercation with Nathan Thompson after 71 minutes, but Swindon were unable to make their numerical advantage count and are four points adrift of the play-offs.
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