Sam Allardyce's men squandered the opportunity to reach their milestone with a victory and were forced to settle for a point, despite dominating the opening 45 minutes.
Bolton took a first-half lead through El Hadji Diouf but were unable to build on it and Portsmouth hit back through Yakubu in a rare attack 18 minutes from time.
Diouf was at the centre of an infamous spitting row in the first meeting between the clubs this season and the legacy of hatred he left behind among the Portsmouth players was evident before kick-off.
Dutch defender Arjan De Zeeuw, whose face Diouf spat in when the sides last met, pointedly refused to shake the hand of his tormenter in the traditional pre-match shaking of hands between the players of both sides.
But Diouf did not appear to be upset by the snub and after 11 minutes he put his side ahead.
The goal stemmed from a misplaced pass by Valery Mezague. Diouf took full advantage and accelerated away from Dejan Stefanovic to beat Jamie Ashdown with a low right-foot shot.
Stefanovic had earlier been named Portsmouth's Player of the Year and after the setback he showed the strength and assurance which were the hallmarks of most of his other performances.
Portsmouth badly missed several injured players and the unhappy crowd only stirred into action after hearing Crystal Palace had taken the lead in the relegation six-pointer against Pompey's bitter local rivals Southampton.
Jay-Jay Okocha screwed a shot into the side netting and Gary Speed mis-kicked from 15 yards with the goal at his mercy.
Portsmouth worried Bolton goalkeeper Jussi Jaaskelainen only once in the first half when he turned a free-kick from Gary O'Neil over the crossbar.
For some reason Wanderers were not the same force in the second half, although Pompey looked unlikely to be able to take advantage until Alain Perrin introduced Ricardo Fuller and debutant James Keene on the hour.
Jaaskelainen caused alarm in the visiting defence when he could only parry a long-range shot from Richard Hughes, but Tal Ben-Haim scrambled the rebound to safety.
Kevin Nolan hit the angle of post and bar with a rasping shot ten minutes after his 55th-minute introduction in place of Stelios Giannakopoulos, but Bolton continued to fail to make the best use of their greater possession.
They paid for this in the 72nd minute when O'Neil took a free-kick on the left and Yakubu bundled the ball in, although several players might also have got the last touch.
It was Yakubu's 17th goal of the season but it could not disguise another moderate performance from the £6million rated Nigerian striker, who is being linked with a summer move to Middlesbrough.
Diouf received unrelenting abuse from the Portsmouth fans and allowed it to get to him in the 82nd minute when he was booked for a wild lunge on Matt Taylor.
The yellow card proved to be too much for Bolton manager Sam Allardyce who could sense more trouble for his petulant, but talented, striker and a minute later took him off the pitch.
A storm of boos greeted Diouf as he left the field to be replaced by Henrik Pedersen, but it proved to be the last notable incident as the game meandered to a draw.
Man of the match: Jay-Jay Okocha.
A busy and aggressive midfield performance from the Nigerian maestro caused Portsmouth plenty of problems.