Alexis Sanchez's status for Chile's Confederations Cup opener is in doubt.
The Copa America holders largely dominated play, though, and Vargas found the net at last late in the first half with a fine finish after being played through by Vidal, only for the referee to controversially cancel the goal for offside after VAR referral.
With time ticking away it appeared that Chile would fail to find the breakthrough their endeavour warranted but Arturo Vidal came up with a goal inside the final ten minutes and Eduardo Vargas capped off a fine performance with a second.
Along with Chile and Cameroon, Group B includes Germany and Australia that will play their match in Sochi on Monday.
African Champions, Cameroon, will today take on Chile in the Match-day two of the FIFA Confederation Cup at the Otkrytiye Arena in Moscow.
La Roja started like a house on fire as Vargas rattled the upright before Fabrice Ondoa denied Fuenzalida inside the opening five minutes.
Vargas finally secured his goal in the 90th minute when he fired home after Sanchez rounded the keeper and saw his shot saved by a defender.
Earlier in the day, a goal scored by Portugal's Pepe at the 21st minute of the group stage match between Portugal and Mexico was also disallowed for offside on review.