Colombia's Santiago Buitrago (Team Bahrain Victorious) crossed the Stage 19 finish line at Tre Cime Di Lavaredo in first place while behind him the battle for the overall lead raged on the fifth and final climb of the day.
Jumbo-Visma rider Roglic attacked with 1km remaining as the gradients ramped up to around 18% but Thomas (Ineos Grenadiers) responded and looked set to extend his lead, only for a final burst by Roglic seeing him take back three seconds.
Thomas will take a 26-second lead into Saturday's penultimate stage, a steep 18.6km individual time trial.
Portugal's Joao Almeida remains in third place in the general standings but lost time in the final kilometre.
Buitrago broke the heart of Derek Gee, accelerating past the Canadian on the final climb to win the stage and leave Gee with his fifth second-placed stage finish of this Giro.
