Armagh were frustrated trying to break down QUB’s defense in the first half and although had most of the possession, they only lead 0-8 to 0-4 at the interval.
After the break, Rafferty collected a high ball and finished into the net to give his side a 1-8 to 0-5 advantage and then Jamie Clarke went on to score a point on his introduction after missing last year’s entire inter-county season.
Armagh remained in control and Duffy’s late goal ensured a comfortable 16-point winning margin for the hosts.
Goalscorers Rafferty and Duffy both scored 1-2 apiece, with Oisin Mac Iomhair (0-4), Conor White (0-1), Stephen Sheridan (0-1) Rory Grugan (0-2), man-of-the-match Aidan Forker (0-2), Ben Crealey (0-1), Jemar Hall (0-2) and Niall Grimley (0-1) the other Armagh scorers.
Martin Clarke was top scorer for Queen’s with four points, with Aaron Morgan, Barry McCann and Aaron McClements also getting their names on the scoresheet.