In a tense and dramatic match at the Morayshire school, Marr looked as if they could clinch a final place again as they led 12-10 in the closing stages but a late surge earned Gordonstoun a penalty that their stand-off Dylan Marshall converted.
He had earlier kicked a penalty and converted his side's only try scored by centre Alan Hunte. Marr outscored their hosts by two tries to one with Andrew McPhilimy and Ry McInnes both going over, one of them converted by their hooker and captain Lewis Anderson.
Gordonstoun await the winners of the rearranged tie between Glenalmond College and Kelvinside Academy which was postponed because of frost. Kelvinside have been hampered by the loss of their outstanding lock forward Scott Cummings who has a shoulder injury and is unlikely to be in the Scotland Under-18 squad for the international matches against England and Ireland.
Elsewhere in the Brewin Dolphin competitions, St Aloysius College lost 47-12 to Stewart's-Melville College in the Shield semi-final, although the match was closer than the scoreline suggests. Stewart's-Melville, who followed up their Shield semi-final win with a 60-0 demolition of Hutchesons' Grammar, will face the winners of tomorrow's semi-final between Robert Gordon's College and Loretto.
Hutchesons' may have lost out at first XV level but their under-16s were victorious against their Stewart's-Melville College counterparts.
Dundee High School, the cup finalists, continued their fine season with a 22-5 win over Glasgow High at Mayfield on Saturday and did so without their captain, Chris Jolland, who made his senior debut for Dundee HSFP at the weekend.