Navy scored two goals in the final 10 seconds of the game to upset the Orange in the Mids' first game at the Dome since 1989.
Varello has been named the league's faceoff specialist four times this season, while Kern has twice been honored by the league.
Navy has now won four consecutive Star Games against Army.
Navy's only lead came when Chris Hill scored the game-winner with 3:27 to play in the contest.
Loyola outscored Navy 10-4 in the second half en route to dealing the Mids their first Patriot League loss of 2018.