The final is now expected to take place at St James's Park against Blyth Spartans.
Aussie winger James Troisi (pictured left) and Wesley Ngo Baheng grabbed the goals
Troisi rocked Whitley with the opener, but in stoppage time Bay won a free-kick on the edge of the box and Lee Kerr put Bay level.
Toon Reserves Make Final!
Obviously it was big moment for Kerr, who was on trial at Newcastle last season and failed to win a contract.
French teenager Baheng, signed from Le Havre, latched on to a Troisi pass in the first period of extra time and scored what turned out to be the winner.