Friday's La Liga clash at Estadio Nuevo Los Carmenes appeared destined to finish in a 0-0 stalemate after an even contest between two mid-table sides.
However, Angola striker Manucho had other ideas, as he came off the bench to snatch all three points for the visitors with what was virtually the last kick of the game.
Manucho was played in by a clever Gael Kakuta pass and the 31-year-old fired low past Roberto with his right foot to give Rayo a second straight away league win.
In a game of few chances, Rayo came closest to scoring before Manucho's intervention.
A rapid breakaway from Paco Jemez's men resulted in Roberto producing a superb one-handed stop to save Lica's curling, 20-yard effort that was heading into the top corner.
Granada huffed and puffed in the second half without threatening Tono's goal regularly, and were cruelly denied a point when Manucho - introduced for Leo Baptistao in the 84th minute - showed his class in front of goal.