Nolan pounced on Linvoy Primus' clearance on 22 minutes to smash a volley past the outstretched arm of David James and end Pompey's perfect defensive record.
It was hard on the hosts who created the lion's share of the chances but failed to capitalise on the oceans of possession they had throughout the game.
An emotional Fratton Park began the evening with a send-off for departing chairman Mandaric who ended his eight-year association with the club after the summer takeover by Alexandre Gaydamak.
Portsmouth manager Harry Redknapp kept faith with the same eleven that defeated Charlton last week.
Despite his goal heroics at The Valley, Lomana LuaLua started on the bench and there was no place for Andrew Cole, who made his first team debut in the midweek Carling Cup victory over Mansfield.
Wanderers boss Sam Allardyce made two changes from the side that played Middlesbrough with Nicky Hunt coming back into defence and Kevin Davies returning up front.
Searching for their first Premiership away win since December, Bolton began the game with a conservative approach - Davies playing in a withdrawn role and Nicolas Anelka left to forage up front on his own.
Pompey had Allardyce's men on the back foot from the start, with Sol Campbell connecting with Matt Taylor's in-swinging corner in the third minute. The former Arsenal man rose highest but could only direct his header wide of the far post.
More was to come though when Kanu and Benjani combined to set Sean Davis up with a clear sight of goal.
Benjani's angled knock-down landed at the feet of the midfielder but, to the dismay of the home support, his volley beat Jussi Jaaskelainen only to rebound back off the post into the Finnish international's hands.
Jaaskelainen was called into action again on 14 minutes when Kanu dallied with the ball on the edge of the area and with minimal backlift took a pot-shot at goal. It looked a relatively comfortable save for the Bolton keeper but he must have seen the ball late as he parried it away to safety.
Gary O'Neil then skipped round Tal Ben-Haim, in his unfamiliar position of left-back, and was able to cross for Taylor who was desperately unlucky to see his right foot volley turned round the post.
As Pompey continued to dominate going forward it was almost inevitable Bolton would take the lead.
Ben-Haim's long distance free-kick was headed away by Primus into the path of Nolan on the edge of the area, and the Bolton skipper wasted no time in sweeping the ball into the corner of James' net.
The approach was decidedly route one, but it proved to be the first goal Portsmouth conceded in 472 minutes of Premiership football this term.
Try as they might to hit back Bolton's back four was resolute until Dejan Stefanovic nipped inside Nicky Hunt on 34 minutes, causing Jaaskelainen to dive low across his goal.
Glen Johnson unwittingly put Benjani clear as he clipped the ball over the top and, as Abdoulaye Faye and Jaaskelainen lost communication, the Zimbabwean nipped in only to see his attempted lob drift harmlessly wide.
On the stroke of half-time Davis burst through from midfield, darting round Ivan Campo and Gary Speed, before unleashing a 20-yard strike which Jaaskelainen was again forced to parry away.
The second half began with Anelka causing an early scare, as the Frenchman out muscled Campbell on the far touchline and drilled a rasping cross-cum-shot which James almost parried into his own net.
Benjani was guilty of the miss of the game after he ran shoulder-to-shoulder with Abdoulaye Meite before shaking off the Ivorian defender. As Jaaskelainen advanced, the former Auxerre man, despite having the time to pick his spot, lashed his attempted finish high and wide into the stands.
LuaLua was introduced just before the hour mark to try and breathe some life into a wilting Pompey attack, with Taylor sacrificed.
It was Bolton though, looking dangerous on the break, who almost put the game beyond doubt when Davies' attempt to play El-Hadji Diouf in was only just thwarted by Campbell.
David Thompson and Manuel Fernandes came on as Redknapp searched for an equaliser but Bolton continued to hold firm.
LuaLua's craft gave some much-needed width and creativity, but too often he overplayed it and left the home fans crying out for a pass.
The impressive Johnson continued his good form by rampaging down the right side, but Faye and Meite proved the equal of his many crosses.
The on-loan Chelsea right-back did have a sight of goal 15 minutes from time but blazed his effort wide of the far post and Bolton breathed a collective sigh of relief.