Wolfe Tones' Derek Collins finished a long ball by Seán Power to the Athenry net.
19-year-old Eugene Cloonan collected a long ball from Paul Hardiman on the left wing and leveled matters after 22 minutes with a point from play.
Another pressure point from a '65' by Cloonan and a volley by Aidan Poniard left the Tones facing a mountain to climb.
Wolfe Tones reduced the deficit to three points, however, in spite of seventeen second-half wides, Athenry held on.
They became the 19th club to win the All-Ireland title, while they were the fourth Galway representatives to claim the ultimate prize.