Aiyegbeni Yakubu headed home 18 minutes from time in what is likely to have been his final home appearance for Portsmouth but could not deny battling Bolton a place in the UEFA Cup.
Victory at Fratton Park would have done the trick for Sam Allardyce's men and they led from only the 11th minute through a solo strike by El Hadji Diouf.
But, although Pompey lacked zest in attack and key players like Steve Stone and Patrik Berger in midfield they found enough to avoid defeat, a scrappy goal by the Nigerian striker - linked with a £6million move to Middlesbrough - saving a scrappy game.
Bolton's European place was assured by Middlesbrough's win over Tottenham but the Champions League is beyond them after Everton's victory against Newcastle.
Diouf's appearance with the Bolton team was greeted by a torrent of boos and - when the players lined-up for the traditional pre-kick-off handshake routine, the fans roared their pleasure as Pompey skipper Arjan de Zeeuw walked straight past the shaven-headed striker.
Bolton boss Sam Allardyce admitted he had considered leaving Diouf out of the line-up to avoid the abuse of the home crowd who clearly remembered the on-loan Senegal striker spitting in De Zeeuw's face at the Reebok last November.
Allardyce, having finally come down on the side of playing Diouf, must have been delighted that he did.
Referee Matt Messias's leniency when the striker late-tackled his Pompey compatriot Diomansy Kamara after 16 minutes was something to behold. And his
only censure was a yellow card late on for a foul on Matt Taylor.
But Allardyce heard just what he expected from the Fratton Park faithful -
non-stop boos.
It made for a tetchy start to the game. Bolton's Gary Speed was fortunate not
to collect a yellow card after twice sounding off at the referee and then
throwing the ball away at a free kick.
But Diouf had a chance to do some damage in the seventh minute even before his
goal when wriggling clear on the left only to overhit his far-post cross as
team-mates arrowed in on goal.
But, after Ben Haim shot well wide from distance, Diouf choked the jeers with
a splendid individual goal in the 11th minute - his ninth of the season.
After a careless pass by Pompey rookie Valery Mezague, a lucky bounce favoured
Diouf 35 yards from goal.
But there was still plenty of work to do and he beat one token challenge
before breezing past Dejan Stefanovic into the area to confound Jamie Ashdown
with a powerful shot.
Then it was a tale of Pompey's sluggish attack against a disciplined Bolton
defence but, after Giannis Skopelitis fired just over the bar, there was little
to cheer the home crowd despite Gary O'Neil's 25-yard free-kick demanding a
tip-over save by Jussi Jaaskelainen.
Jay Jay Okocha and Speed had better opportunities in Bolton's breakaways
before the break but plucky goalkeeper Jamie Ashdown kept them out.
Pompey seemed happy enough with Yakubu's scrappy equaliser to save a scrappy
match, applying the final touch in the 72nd minute from a pin-ball free-kick by
O'Neil.
A quite dreadful game went from bad to worse in the second half with all
continuity masked by a blur of substitutions and the crowd more interested in
jeering Diouf and taking the rise from news of Crystal Palace's goals against
Southampton.
The striker received an inevitable booking for a bad foul on Matt Taylor
before his slightly early substitution.
He was lucky it was not a red card but Allardyce seemed more upset about an
incident a few minutes earlier when Ashdown appeared to land a blow on the legs
of striker Kevin Davies in response to a kick at the ball that was in the
keeper's arms.
Allardyce had to be steered back to the bench by fourth official Phil Crossley
and a steward.
Teams
Portsmouth Ashdown, Primus, De Zeeuw, Stefanovic, Taylor,
Mezague (Cisse 77), O'Neil, Skopelitis (Fuller 60), Hughes,
Yakubu, Kamara (Keene 60).
Subs Not Used: Hislop, Rodic.
Goals: Yakubu 72.
Bolton Jaaskelainen, Candela (Jaidi 76), N'Gotty, Ben Haim,
Gardner, Hierro, Giannakopoulos (Nolan 55), Okocha, Speed,
Diouf (Pedersen 84), Davies.
Subs Not Used: Poole, Fadiga.
Booked: Gardner, Diouf.
Goals: Diouf 11.
Att: 20,188
Ref: M Messias (S Yorkshire).