With Serbia eliminated earlier in the tournament, former Wimbledon champion Djokovic caused a stir when he said he would support Croatia in their semi-final against England.
Croatia went on to beat England 2-1 and face France in the final on Sunday.
Taking a break from preparing for the showdown with France, Barcelona star Rakitic told Djokovic's critics to leave him alone.
"I tip my hat to him, I root for him at Wimbledon. I would like to see him play the final so on Sunday we both have a great day," he said.
"We are human beings and we have to try and put history behind us.
"For me Nole is a fantastic athlete but even more a fantastic person. I wish him all the luck in the world."
Tensions between Serbians and Croats have run high for years and Vladimir Djukanovic, an MP in the ruling Serbian Progressive Party, went on social media to berate Djokovic.
"Only idiots can support Croatia. Aren't you ashamed Novak?" he wrote.
Djokovic is currently at Wimbledon, with his semi-final against Rafael Nadal scheduled for later on Friday.