In what was a more open encounter than the initial clash between the sides at the Athletic Grounds which resulted in a 0-14 to 0-14 stalemate, Armagh made arguably the better start with Aaron Findon's goal helping them to an early two point lead.
However, Monaghan soon set about reducing the deficit and outscored their opponents by five points to two before Conor McManus got in behind the Orchard defence to fire past Phillip McEvoy and into the net.
The Farneymen were well in control at this point and led by four at half time and soon stretched that to seven, but Armagh battled gamely to keep in touch with the hosts.
Jamie Clarke weighed in with five points while Tony Kernan landed seven - but it was McManus who had the final say with four scores towards the end of the game to seal victory by 1-18 to 1-13.
Armagh are set to learn their fate in the qualifiers on Monday, while Monaghan will defend their Ulster title against Jim McGuinness's side on 20 July.