Kovac's men were eliminated from the FIFA World Cup on Monday after conceding three late goals at the Arena Pernambuco in Recife.
Needing a win to progress, Croatia were more attacking in the second half but they were punished as Mexico hit on the counter-attack.
Barcelona signing Rakitic stayed as the deepest of Kovac's midfielders, and the 42-year-old said he felt that was best for his team.
"When everything goes well, it's OK. When it doesn't, everyone has their say. I thought it was best we play like that, without a classic defensive midfielder," Kovac told HRT.
"I'm the coach and I decide. We're not that much weaker than Mexico like the result indicates. Heads up, we go home."
Rafael Marquez, Andres Guardado and Javier Hernandez scored for Miguel Herrera's men, while Ivan Perisic netted a consolation goal for Croatia and Ante Rebic was sent off for a rash challenge.
Kovac said his ideal formation of 4-1-4-1 failed to work in the first half.
"We wanted to play 4-1-4-1. I wanted to release (Ivica) Olic of his defensive responsibilities so he could play more attacking," he said.
"It didn't work so we replaced (Danijel) Pranjic and (Sime) Vrsaljko, and brought in (Mateo) Kovacic. As soon as we opened up, you saw how good a team Mexico are."
Kovac said his team may have struggled with their fitness in the second half, but praised Mexico for being the better side.
"Mexico had respect for us. They didn't press as they normally do," he said.
"Maybe we fell physically in the second half, but we have to say they were better."
