Ryan Keenan did edge Fermanagh ahead with a free but two scores from Steven McDonnell and one by Kieran Toner gave Armagh the lead.
Armagh then got their first goal which came after a Toner's blocked shot fell to Brian Mallon who slipped the ball to Moriarty who fired it into the net.
Fermanagh responded with points from Ciaran McElroy and Mark Little but a McDonnell free left them 1-5 to 0-4 behind at the break.
Any thoughts of a Fermanagh revival were snuffed out just 54 seconds after the restart when Armagh netted their second goal.
A good build-up involving Charlie Vernon and Brian Mallon ended with Clarke shooting the three-pointer.
Interview: Steve McDonnell
McDonnell landed another fine score from play but Fermanagh, with Barry Owens on for Shane McCabe, got a much-needed point through Martin McGrath.
Fermanagh got a goal in the 45th minute to keep the contest alive.
McGrath's effort fell short and Maguire came in to fist into the net.
That meant Armagh's lead was down to four points but they got the next score with the majestic McDonnell again doing the business from play.
Shane McDermott and a long-range effort from Ciaran McElroy added to the Erne County's tally before McDonnell took his personal tally to six.
That had Armagh three ahead but McGrath pointed from play, Little landed another free and then came Doherty's equaliser which was the least Fermanagh deserved.
Armagh: P Hearty, A Mallon, F Bellew, F Moriarty, A Kernan, A O'Rourke, C McKeever, P McGrane, K Toner, C Vernon, B Mallon, M O'Rourke, S McDonnell, R Clarke, S Kernan.
Fermanagh: R Gallagher, S Goan, S McDermott, P Sherry, D Kelly, R MCCluskey, T McElroy, M McGrath (c), M Murphy, C McElroy, J Sherry, R Keenan, E Maguire, S McCabe, M Little.
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