The AC Milan striker complained of back pain when he was asked to come on in the 85th minute of play which did not convince Dalic.
Dalic revealed that Kalinic also declined to enter a warm-up friendly against Brazil in England earlier this month, and that he said he was too injured to train on Sunday.
Croatia striker Nikola Kalinic will reportedly be sent home from the World Cup after telling management he was unable to come on as a substitute during Saturday's Group D win against Nigeria in Kaliningrad.
Dalic did not answer any further questions or go into the matter any further. "However, he then stated he wasn't ready to come on due to a back issue".
Saturday's clash against the Super Eagles marked Kalinic's fourth successive game starting on the bench under Dalic, who went with Mandzukic and Andrej Kramaric in attack, with Ivan Perisic and Ante Rebic flanking them.
"I have calmly accepted that, and since I need my players fit and ready to play, I have [to make] this decision".
Kalinic's exit has since exposed Croatia's lack of attacking options, with Mandzukic the only out-and-out striker available in their squad.
The news will sour what had been a positive start to the tournament after Luka Modric had scored from the penalty spot to seal all three points for Croatia after an own-goal from Oghenekaro Etebo had handed Dalic's side the lead.
The short-handed Croatian squad will take on Argentina on Thursday, where an upset win would punch the team's ticket to the knockout stage of the tournament.
Phil Mickelson to critics after U.S. Open penalty: 'Toughen up'
And if that's the way people took it, I apologize to them, but that's not the way it was taken. He carded a 10 on the hole for a 5 over par.