Flares were thrown on the pitch by fans in the Croatian end in the second half of the match, forcing referee Mark Clattenburg to delay the game.
Tomas Necid converted a penalty after the restart to deny Rakitic's team victory but the Barcelona midfielder fears the result may prove irrelevant if UEFA take action.
"We have to see if we will play against Spain, maybe they will send us home after this," he told HTV after the final whistle.
"There are a lot more fans that love the national team and they will not be able to see Croatia play.
"It is hard to say, but we feel more comfortable playing away... we were lucky that the match went on, the referee wanted to end it immediately."
Croatia are top of Group D with four points but a win for Spain against Turkey would see the reigning champions rise into first place.