The Frenchman attacked on the short, sharp closing climb and held off the closing peloton to take the stage win and build on Deceuninck-QuickStep's strong start to the season.
Alaphilippe finished ahead of Simone Consonni and Peter Sagan, but had time to look over his shoulder and celebrate across the line after an attack that hinted he's ready to repeat his fine form from a 2018 season that saw him claim the mountains classification at the Tour de France.
Vuelta a San Juan
Bennett comes from back of bunch to win sprint in final stage
The result means that Alaphilippe trails Fernando Gaviria by just three seconds going into the Stage 3 time trial.
A strong field has entered the Vuelta a San Juan as the 2019 cycling season limbers into action, with Alaphilippe's Deceuninck-QuickStep team-mate Evenepoel Remco among a star-studded field. The youngster came in at 15th on the day, still well-placed in General Classification.