Both teams were hampered by injury and Lovat's Drew Howie limped off after just two minutes as his damaged ankle flared up.
But two minutes later Lovat were in front when Greg Matheson bustled through the Glen defence and rifled home from a narrow angle.
In the 10th minute Lovat's Lorne MacKay wasted a good chance as he snatched at a loose ball in the penalty area. Two minutes later Glenurquhart's Lewis MacLennan passed up a half chance to get his side on level terms.
Lovat had the upper hand in midfield and Matheson was increasingly threatening, but in the 25th minute he was forced out after being downed in the box by the Glen's Fraser Heath.
Lovat supporters screamed penalty, but referee Innes Wood was unmoved and booked Lovat's powerful midfielder Ryan Ferguson for his remonstrations.
Two minutes later Lovat doubled their lead with Kevin Bartlett popping up to guide the ball home from inside the box.
Glenurquhart looked devoid of ideas and five minutes later Lovat's Graeme MacMillan swept home the ball from 20 yards after another precision attack.
The Glen half-time talk had some effect as they began to threaten the Lovat goal for almost the first time.
But in a sweeping counter-attack, MacMillan struck the upright with the keeper beaten, then an uncharacteristic blunder by the Glen's international full-back John Barr in the 63rd minute let Lorne MacKay cash in with a crisply-hit shot from the edge of the penalty area.
The goal appeared to drain the fight from the Glen, but they found renewed energy and in the 72nd minute captain Eddie Tembo let fly from distance only to be denied by a fine save by Lovat keeper Stuart MacDonald.
MacDonald frustrated the Glen just as he had in last year's final, but in the 84th minute he was finally beaten by a Lewis MacLennan strike.
With the match into added-on time Lovat forced a free hit and from a well-worked routine the ball was played through to MacKay in space and he blasted home to complete the scoring.
Ferguson, a deserved man of the match, said: "We were quietly confident, but no-one could have predicted this result.
"We knew we had to be at our best and to retain the trophy is just unbelievable."