The 32-year-old forward was the provider as Chris Hackett got the ball rolling for the Lions early on and then scored his sixth of the campaign to make it 2-0.
Former Stevenage striker Steve Morison added a third after the break as Millwall returned to winning ways, with Jordan Rhodes grabbing a consolation for Huddersfield.
The Lions got the first after 11 minutes when Harris's through ball eluded the Terriers defence but not Hackett, and his right-foot shot was too powerful for goalkeeper Alex Smithies.
Top scorer Harris - who overcame the calf injury that forced him off against Gillingham last weekend - doubled the lead two minutes later with a close-range header from David Martin's cross.
Any hopes of a Huddersfield comeback were extinguished just five minutes after the interval when Morison rose highest to head home Hackett's corner. Rhodes notched a late consolation for the visitors when he turned and shot following Lee Novak's flick but it was not enough to stop Town's four-match unbeaten run coming to an end.