Vagenas fills one of the two vacancies created by Arena's appointment last week as head coach of the US national team.
Vagenas fills one of the two vacancies created by Arena's appointment last week as head coach of the United States national team following the sacking of Jurgen Klinsmann.
There is still no word on who is likely to take over the coaching duties from Arena, who was both head coach and general manager for the Major League Soccer powerhouses.
Galaxy President Chris Klein said Vagenas, born and raised in Los Angeles, was the logical choice for promotion to GM.
"In each of his roles with this club - team captain, Academy Director and VP of Soccer Operations - he has consistently shown an unparalleled dedication and expertise," Klein said.
"We will continue to fill our front office with qualified and innovative individuals and we have full confidence that Peter will excel as our General Manager and Vice President of Soccer Operations," he added.
Vagenas made his debut for the Galaxy in 2000, later going on to captain the side to victories in the MLS Cup and US Open Cup in 2005.
A 13-year playing career in the MLS also included spells with the Seattle Sounders, Vancouver Whitecaps and Chivas USA.