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Chances proved to be rare for the remainder of the first half, with Alan Connell's coming closest to drawing level for the hosts when he fired over from the edge of the box.
Rochdale started the second half impressively and deservedly doubled their lead in the 54th minute when Matthew Lund converted after finding some room between Northampton defenders.
However, Lund's joy was short-lived as he received a second yellow card just moments later when the referee took exception to how he celebrated Rochdale's second goal of the evening.
The visitors refused to offer Northampton any hope of an unlikely comeback and managed to extend their lead further just after the hour mark when Joe Bunney completed a counter-attack by firing home from a tight angle.
Northampton failed to respond after conceding a third goal and they were lucky not to be beaten by a wider margin as Henderson headed wide in the closing stages.