Halilhodzic, who was appointed to the post earlier this month, excluded the 35-year-old Endo from the Japan squad that will face Tunisia and Uzbekistan, asserting that it was time to look to the future.
"You will notice one name missing from the list," Halilhodzic told reporters. "Yasuhito Endo has made a huge contribution to Japanese football. I have come here for the project of building for the 2018 World Cup in Russia. But we must not forget Endo's contribution and he deserves respect for what he has done for Japan."
Endo's run with Samurai Blue ends with the Gamba Osaka midfielder having featured for Japan on 152 occasions.