The Deceuninck-QuickStep rider set the fastest time around a short ITT course to continue his team's remarkable start to the season.
And there was more good news for Deceuninck as Alaphilippe's young team-mate Remco Evenepoel secured his first ever podium position since turning professional.
Vuelta a San Juan
Bennett comes from back of bunch to win sprint in final stage
Stage 2 Report
Julian Alaphilippe launched a solo attack on the final climb to win Stage 2 of the Vuelta a San Juan.
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.
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.