Barcelona's Rakitic came off in the 67th minute of the 3-2 home win over Spain which gave Croatia the chance to top League A Group 4 and claim a place in next year's four-team finals.
"He will go to Barcelona, it's a serious injury. You know that I usually take no risk. If there is a doubt that the injury could be serious, then we let him rest," Dalic told Sky Sports.
"We want healthy players and Ivan in this moment is not 100 percent ready. Unfortunately, we are going to play without him."
Rakitic, 30, has played 102 games for Croatia but Dalic said they have players capable of filling in.
"We will see who will replace him. We have (Mateo) Kovacic, we have (Josip) Brekalo, we have (Milan) Badelj," he added.
"There is always a solution and we should stop whining about someone who's not going to be there. We will find a solution and we are going to Wembley to enjoy football."
The winners will qualify for the Nations League semi-finals with the losers being relegated to League B. A draw would see leaders Spain clinch top spot in Group 4.
