Ivan Klasnic put the Trotters ahead in the 79th minute when he diverted a bouncing Matt Taylor ball past Tim Howard and it seemed like it would be enough, especially when Everrton's Marouane Fellaini was sent from the pitch with four minutes remaining when he kicked out at Paul Robinson in response to a strong challenge.
But Beckford popped up to score his first league goal for the club with a deft chip from the edge of the box in added time which saw the Toffees go 12th and Bolton move to 6th.
Everton Tim Howard (gk), Phil Jagielka, Sylvain Distin, Leighton Baines, Phil Neville (Yakubu 81'), Mikel Arteta, Marouane Fellaini, Tim Cahill, Steven Pienaar, Diniyar Bilyaletdinov (Coleman 67'), Louis Saha (Beckford 81')
Subs - Jan Mucha (gk), Seamus Coleman (67'), Yakubu Aiyegnbeni (81'), Jermaine Beckford (81')
BoltonJussi Jaaskelainen (gk), Zat Knight, Gary Cahill, Paul Robinson, Gretar Steinsson (Ricketts 59'), Stuart Holden, Fabrice Muamba, Matt Taylor, Lee Chung-yong, Johan Elmander (Klasnic 62'), Kevin Davies
Subs -Adam Bogdan (gk), Samuel Ricketts (59'), Ivan Klasnic (62')