Forgotten man Ivica Mornar gave the visitors the lead at Nene Park after only 11 minutes, but Portsmouth found their League Two opponents difficult to break down, and it wasn't until the 72nd minute that Pompey added to their talley when a suspicious looking goal from Gary O'Neil, who seemed to be offside, put the game beyond the Diamonds.
Rushden did get a late goal through Alex Hay to give themselves a deserved consolation in what was a very unconvincing display from Portsmouth.