Northampton winger Chris Hackett also missed a penalty to deny Aidy Boothroyd's side a crucial win.
But the Shakers went in front in the 23rd minute when Ricky Ravenhill fouled Craig Jones inside the area and Nardiello thumped the spot-kick home.
Despite the hosts' dominance, Northampton scored a shock equaliser in the 29th minute when Howell headed Hackett's free-kick into his own net.
Then Hackett missed from the spot in the 45th minute, blazing over after William Edjenguele had upended Izale McLeod.
Duke made a stunning reaction save just after half-time, keeping out Nardiello's first-time volley from a Tommy Miller pass.
At the opposite end, Brian Jensen superbly denied McLeod at point-blank range and Mathias Doumbe missed a golden chance late on.