The 23-year-old will undergo a medical and put pen to paper on a four-year contract with the Bluebirds on July 25, after he has made his final appearance for NK Maribor in a Champions League qualifier.
Velikonja scored 20 goals in 46 appearances for the Slovenian champions, who beat Rangers to qualify for the Europa League last season.
City boss Malky Mackay told the club's official website: "We're really excited to be bringing in an international striker to complement our squad.
"Etien is a player I tried to sign once before and have keenly followed his progress with Maribor. We felt the time was right to bring him to the UK and I'm looking forward to seeing his career continue to develop with Cardiff City."