Quayle pounced seven minutes from time to prod home a Jimmy Kelly cross and send the non-league side into delirium.
The Seadogs seized their big chance and piled on the agony for Third Division strugglers Southend in the third-round replay. The Shrimpers were denied by a sensational second-half save from Boro goalkeeper Leigh Walker who also blocked Jay Smith’s injury-time free-kick as the pressure reached breaking point.
Boro had shaded the opening stages against their opponents at a packed McCain Stadium. Southend were slow to start but once midfielder Mark Gower found his range they began to assert some degree of authority.
Leon Constantine tested the home defence for the first time in the 15th minute but lofted his final shot way over Walker’s bar. Boro’s leading scorer Quayle had a great chance just past the half-hour when he was played onside by the visitors’ defence and strode clear only to fluff his final shot.
Moments later inspirational home midfielder Kelly also stretched the Southend defence but the experienced Darryl Flahavan saved the day.
Boro finished the first half with a flourish when Ashley Lyth sent Scott Kerr through on the right, only for him to screw his shot wide of the left-hand post. The league side should have stolen the lead in the 72nd minute when Tesfay Bramble seized on a loose ball only to blaze over from the edge of the six-yard box.
Scarborough’s lively approach to the second half finally paid dividends with seven minutes to go when Quayle poked home the simplest of chances.
Southend boss Steve Tilson flung on his forwards in a bid to save the day. But Boro hung on, and the final whistle was greeted with jubilation.
SCARBOROUGH: Walker, Lyth, Cryan, Baker, Hotte, Sestanovich, Kerr, Kelly, Marcelle, Whitman, Quayle.
SOUTHEND: Flahavan, Jupp, Cort, Hunt, Stuart, Gower (Steven Clark 87), Smith, Maher, Jenkins (Kightly 89), Bramble (Corbett 86), Constantine.
Referee: B Curson (Leicestershire).