Kovac handed debuts to four players for the friendly against the South Americans, with Croatia taking on Italy in a crucial Euro 2016 qualifier on Sunday.
Both Group H pacesetters boast 100 per cent records in qualifying and Anas Sharbini's first international goal looked set to send Kovac's men into the clash off the back of a win.
However, a deflected Cristian Ansaldi strike coupled with Lionel Messi's penalty ensured Gerardo Martino his third win since taking the reins from Alejandro Sabella.
Despite the defeat, Kovac was pleased with the effort of his players and stated his team selection was the correct one with the weekend's competitive clash on the horizon.
"The players [that] played today are 'no names' but we have a match on Sunday against Italy in Milan and it's very important for us," he told beIN Sports.
"I decided to let the [other] players work with my brother and assistant coach [Robert]. Sorry for that, but I thought the players who played today did a good job and I'm proud of them."
On the subject of the lack of star names such as Luka Modric, Mario Mandzukic and Ivan Rakitic he added: "They are playing every third day with their clubs so it's hard to play a match such as this before Italy.
"I think it's the best way to give them the best amount of time to recuperate as we are preparing them for Sunday."
