Kevin Small and Declan Cassidy starred for Mary's as they held off a second-half fightback to pull clear again.
St Mary's led 0-8 to 0-6 at half-time and extended their advantage to five points after the resumption.
Colman's cut the margin to three and had a strong 55th-minute penalty claim turned down when three in arrears.
Instead, the referee awarded a 13-metre free after Rian O'Neill looked to have been hauled down in the large square.
After O'Neill got up to point the placed ball to reduce the margin to 0-15 to 0-13, Magherafelt hit back with the final four points to seal a deserved victory after losing two previous finals.
Goalkeeper Odhran Lynch performed heroics for St Mary's as he made three great saves, in addition to delivering a series of accurate kickouts.
St Mary's full-forward Small showed a portent of what was to come as he slotted the opening score after soaring to win possession.
However after lead 0-3 to 0-1, St Mary's were held scoreless for 15 minutes as a Matthew McCreesh point nudged Colman's into a 0-4 to 0-3 lead.
But a superb Conall Devlin point from a tight angle got St Mary's back on track as they hit five out of the remaining seven scores before the break to take a 0-8 to 0-6 lead.
Despite playing against the wind, St Mary's hit three unanswered points on the resumption to move five ahead as Small continued to wreak havoc in the Colman's defence.
Magherafelt still looked in comparative control at 0-14 to 0-9 ahead after 48 minutes points but points from Crossmaglen duo Rian O'Neill and Cian McConville quickly had only a kick of the ball between the teams again.
As Colman's began to rain in wind-assisted high balls into the Mary's defence, the game threatened to turn and the Newry school will feel extremely hard done about the 55th-minute penalty call.
But nonetheless, St Mary's were the better side for most of the game and substitute, Tiernan McAteer and the influential Small were among the late scorers as Magherafelt hit the final four points.
St Mary's Magherafelt clinched their first MacRory Cup title as they beat 19-times winners St Colman's Newry 0-19 to 0-13 in the final at Armagh.