The goals only told part of the story. West Ham defender Tomas Repka was shown a red card just before half-time for a headbutt on PNE midfielder Brian O’Neil.
North End manager Billy Davies had to watch the last few minutes of the game from the stand after being ordered to leave the touchline because of some over exuberant behaviour.
At full-time it was a hive of activity down the tunnel with stewards and police having to go in to sort out a fracas involving players from both teams.
An action-packed afternoon from start to finish then but a successful one in the East End for the visitors, the victory seeing them strengthen their footing in the play-off race.
They indeed reach the play-offs and met West Ham in the final at the Millennium Stadium two-and-a-half months later, a game the Londoners won 1-0 to clinch promotion.
The March meeting was a deserved three points for North End, though, with them leading from early in the contest which was played in front of a 26,000 crowd.
Nugent put them in front after 17 minutes, taking advantage of a slip from home keeper Stephen Bywater.
When a back pass was played to him, Bywater took a heavy touch and Nugent didn't need a second invitation, nipping in to take the ball round the keeper and roll a shot into the empty net.
Repka got a straight red in the 43rd minute for laying out O’Neil in the centre-circle, that causing a coming together of players.
North End’s second goal came nine minutes from time, substitute Patrick Agyemang’s first touch since coming on being to control a pass on the left hand side of the box.
His second was to take the ball inside a defender, his third touch being a low shot into the far bottom corner.
Bobby Zamora volleyed home a Marlon Harewood cross three minutes later but PNE held out for victory.