Owen Coyle's side struck twice in two first-half minutes through Ivan Klasnic and Kevin Davies to put themselves in the driving seat at the interval.
But Aruna Dindane's double earned crisis-club Pompey a well-deserved draw and left Wanderers still needing a point from their remaining two games to be absolutely certain of safety.
Bolton could have been in front as early as the fourth minute when David James fumbled Matt Taylor's free-kick but Gary Cahill's follow-up effort clipped the outside of the post.
The Portsmouth goalkeeper atoned for his early error with fine saves to keep out Taylor's header and then Klasnic's shot on the turn as the Trotters piled forward in the opening stages.
But despite the home side's dominance, Jussi Jaaskelainen was called into action when he produced a smart stop to deny John Utaka's low drive.
Bolton took the lead on 26 minutes when Klasnic got in front of his marker to head home Jack Wilshere's inviting cross.
Two minutes later, Davies doubled Wanderers' advantage with a goal created superbly by Vladimir Weiss.
The on-loan Manchester City winger, making his first start for Bolton, set off on a magnificent run from the halfway line, beating at least four Pompey players before squaring for Davies to tap home.
The FA Cup finalists nearly responded immediately but Tommy Smith's 25-yard drive struck the foot of the post.
The visitors reduce the deficit 10 minutes after half-time when substitute Frederic Piquionne picked out Dindane and he scuffed his shot past Jaaskelainen.
And the Ivory Coast striker grabbed a 68th-minute equaliser when Utaka pounced on Gary Cahill's slip to cross for Dindane to volley home.
Davies nearly nicked it for Bolton deep into injury time but the Whites captain saw his header come back off the upright.