Cahill leapt above a static Pompey backline two minutes from time to settle an exciting but low-quality encounter between two sides seemingly destined for the Premier League drop.
Pompey defender Younes Kaboul had cancelled out Tamir Cohen's opener before Matt Taylor fired a penalty against his former club to earn Bolton a half-time lead.
Debutant Kevin-Prince Boateng looked to have the home side a point, stroking his first goal for the club following his summer switch from Tottenham but it was Cahill who had the final say.
Hart handed debuts to Boateng, Tal Ben Haim and Jamie O'Hara and disjointed Pompey looked shaky from the start as first Sam Ricketts' cross picked out Cohen, only for the midfielder to be denied by David James.
Then Gretar Steinsson's through ball found Taylor running beyond the home defence but he sliced horribly wide.
Pompey failed to learn their lesson and took the lead through another Steinsson pass, this time discovering Cohen in far too much space and the Israeli was not as wasteful as Taylor, firing into the roof of James' net.
The slight suspicions of a feel-good factor sweeping round Fratton Park following Sulaiman al-Fahim's takeover soon disappeared as the enormity of the situation they face this season.
Kaboul's powerful header from O'Hara's fine delivery gave them some cheer, but it was a memory of the past that continued the gloom going into the break.
Nadir Belhadj was inexplicably robbed by Fabrice Muamba inside his own half and the England under-21 midfielder fed Kevin Davies who was clumsily clattered by Ben Haim, with Taylor converting from the spot.
The second half failed to match the intensity of the first as Bolton looked content with their lead and Pompey were rapidly running out of ideas.
However Boateng forced the issue, sweeping home from 12 yards after O'Hara's shot was blocked, but while the home side should have gone on to win the game with the momentum on their side, Cahill crashed the party.
Jlloyd Samuel's long throw was not adequately cleared and as each side exchanged head tennis, Cahill diverted his crucially wide of James' left hand.