"I am sorry things panned out like this and I am really surprised by Jelavic’s course of action, but I accept his decision," Kovac told the Croatian Football Association’s official website (www.hns-cff.hr) on Saturday.
"I wish to thank him for everything he has done for the national team and I can only wish him the best of luck in life and in the rest of his club career."
The 29-year old striker, who joined England's Hull City this year after two years at Everton, scored six goals in 36 appearances for Croatia having played second fiddle to Mario Mandzukic throughout his international career.
Against the Bulgarians, Jelavic was twice instructed to warm up but Kovac, often criticised by Croatian media for his tactics which they say led to an early World Cup exit, decided to keep him on the bench.
The Croatians are joint top of Group H with Italy on six points from two games ahead of their next qualifier at home to Azerbaijan on Monday.
(Writing by Zoran Milosavljevic in Belgrade; Editing by Mark Meadows)
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