Reports emerged earlier on Monday that Kalinic had refused to come off the bench during his country's opening 2-0 win over Nigeria in Group D, citing his back complaint.
Speaking after Saturday's match, Dalic told reporters his side had finished the 90 minutes without injuries but "with a problem".
However, Dalic told a specially arranged news conference that Kalinic would depart Croatia's team base in Roschino but due to recurring back spasms, as opposed to any disciplinary issue.
"During the Nigeria encounter, Kalinic was warming up and was supposed to come on in the second half. However, he then stated that he wasn't ready to come on due to a back issue," Dalic said.
"I have calmly accepted that, and since I need my players fit and ready to play, I have [to make] this decision."
The 30-year-old's absence means Croatia lack a specialist alternative to Mario Mandzukic, although Andrej Kramaric – who started the Nigeria game playing off the Juventus man – can lead the line if needed.
Croatia are back in action against Argentina in Nizhny Novgorod on Thursday.