Barry Owens, who was returning for Fermanagh after heart surgery, scored the vital goal on 54 minutes with his first touch after coming on as a substitute.
However, O'Rourke acknowledged that the outcome could have been different if Ronan Gallagher had not saved Conleth Gilligan's penalty when Derry were leading 1-3 to 0-1.
"We knew if we conceded the goal it would have been an uphill battle but once it was saved we knew we had the fitness to come through.
"The boys were tremendously fit and our fitness coach Leo McBride hasn't got the praise others have.
"With Barry it is just one of those things you take a gamble on - sometimes it works and sometimes it doesn't and this time it worked."
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