A ninth successive home win would have capped a remarkable turnaround for a team placed 20th at the start of February and one point looked like being enough until Anthony Knockaert gave Leicester a last-gasp 3-2 win over Nottingham Forest to secure sixth place for the Foxes.
Blackpool attacked with a verve rarely seen since their stint as early season pace-setters and fine goals from Matt Phillips and Ludo Sylvestre had them 2-0 up after 35 minutes.
That lead appeared safe as the interval approached but Chris Eagles and recalled striker Craig Davies were on hand to haul Wanderers level.
Darren Pratley and Lee Chung-Yong passed up chances to give Bolton the win they ultimately needed - misses they were left to rue after Knockaert's late intervention.
Phillips ensured Blackpool started on the front foot - firing a speculative effort into the side-netting, forcing Whites full-back Marcos Alonso to scramble behind and dragging wide after bursting clear all inside the first four minutes.
Simon Cox's early goal for play-off rivals Forest meant Bolton had to find their feet, and they did as a pair of left-footed, in-swinging set pieces from Rob Hall - the on-loan West Ham youngster handed a surprise debut by Freedman - caused unease in the Blackpool penalty area before Davies hooked a volley from Eagles' left-wing corner over the bar.
But Blackpool made the breakthrough in stunning fashion after 21 breathless minutes - Phillips emerging from slick one-touch interplay involving Tom Ince and Gary Taylor-Fletcher to lash left-footed into the top corner.
Bolton came close when Matt Gilks managed to parry Lee's low drive away from the in-rushing Davies, but Blackpool retained their threat and Gilks' opposite number Adam Bogdan was out quickly to curtail a typically menacing run from Philips after the half hour.
The hosts soon had a mountain to climb after Paul Ince's side once more benefited from static defending with aplomb - Neal Eardley's lofted cross to the edge of the area was crisply volleyed home as Sylvestre claimed a fourth goal in six matches.
In an attempt to turn things around, Freedman sent on striker Marvin Sordell in place of Hall eight minutes before the break and his team unleashed a staggering turnaround in injury time.
Two of the outstanding performers in Bolton's late-season rally combined to reduce the arrears as Chris Eagles arched an excellent side-footed finish into the top corner from 18 yards after Alonso raided down the left.
In the last act of the half, Davies' hopeful strike from distance took a wicked deflection off Stephen Crainey to leave Gilks with no chance and send the Reebok Stadium into raptures.
The momentum kept up after the break. Davies and Eagles tried their luck from distance but an open game equally suited Blackpool, for whom Ince's influence was growing.
Shortly after the hour, Lee chipped back into the Seasiders' area from an Eagles corner and Gary MacKenzie produced an acrobatic clearance as Davies and Sordell looked to bundle home.
Bolton were firmly in the ascendancy as the game entered its final quarter and Gilks did well to push Alonso's 30-yard free-kick clear.
In the 80th minute, the impressive Pratley broke up play to feed Lee, who cut inside Blackpool substitute Isaiah Osbourne to find a return pass but the former Swansea midfielder blazed high and wide.
Lee was guilty of a more glaring miss in the 84th minute, brushing the side-netting after Eagles found him with space and time inside the area.
Hearts were in mouths at the other end when Bogdan tipped over a rasping Sylvestre strike from the corner of the box but worse news arrived from the City Ground.
Wanderers surged forwards once more during five additional minutes but David Wheater could not turn home a cross from fellow sub Tom Eaves, leaving them agonisingly short.
- Sports & Recreation
- Craig Davies
- Chris Eagles
- Anthony Knockaert
- Matt Phillips