Rock, whose goal was scored by Paudie Ward, led early in the second half but Glenbeigh-Glencar won 1-14 to 1-11 after a close tussle at Croke Park.
Rock's Enda McWilliams was dismissed for two yellows in the first half.
The Tyrone men ended with just 12 men as Niall Mullan and Diarmuid Carroll got second bookings late in the game.
Glenbeigh's Daniel Griffin had been shown a straight red before the break.
It was the second the small rural club from Tyrone had lost an All-Ireland Club JFC final at GAA headquarters.
They lost in the 2008 decider and had high hopes of winning the trophy this time.
However, it was Kerry side Glenbeigh-Glencar who finished strongly to take the title at the end of a drama-packed decider.
The Munster champions got off to a flying start when Kerry star Darran O'Sullivan fired in a goal, but the Red Hand men fought back with points from Aidan McGarruty, Conor McCreesh and Ciaran Gourley.
Glenbeigh had attacker Griffin sent off, and Rock finished strongly with scores from Aidan Girvan and McGarrity to draw level at 0-9 to 1-6 at the break.
McGarrity gave Rock the lead for the first time, and Ward's 48th minute goal gave them genuine hope.
But the late dismissals of Mullan and Carroll, both on second bookings, and Enda McWilliams (yellow/black) was a major blow.
The Kerry men finished with points from O'Sullivan and Jason McKenna to take the title.
Tyrone team Rock St Patrick's had three players sent off as they lost Sunday's All-Ireland Junior Club final to Glenbeigh-Glencar of Kerry.