The switch comes on the eve of Croatia's participation in the tournament opener against hosts Brazil in Sao Paulo, after coach Niko Kovac confirmed the recurrence of an ankle injury for Mocinic.
It is believed the 21-year-old HNK Rijeka midfielder will be sidelined for two to three weeks.
Hamburg's Badelj, who was himself initially ruled out of the World Cup through injury, will miss the Brazil match as he is set to join Kovac's squad on Friday.
Croatia revealed the approval of Badelj's call-up on their official Twitter feed.
A message read: "FIFA allowed Croatian team to replace injured Ivan Mocinic with Milan Badelj who will join the team on 13th."
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