Bonačić is known as coach who gives young talented players a chance. In the 1992–93 season, when he was NK Pazinka coach, he launched the career of Dado Prso, the former Rangers and Monaco striker. Also whilst at Slaven Belupo, he started the career of young central defenderIvica Križanac who currently plays for FC Zenit in Russia. He was selected as Croatian Coach of the Year in 1996 when he reached the final of the Croatian Cup with middle-class Croatian club NK Varteks. In 1996, he won with Varteks against Dinamo Zagreb 4–3. Thanks to his success with NK Varteks Varazdin, in the 1997–98 season he became head coach of top Croatian club Hajduk Split. Soon after Bonačić's appointment, however, the management board named coach Tomislav Ivić as Bonačić's assistant. Ivić preferred defensive football and young coach Bonačić preferred attacking football. As a result, the team had a conflict of tactics. After ten match days, Hajduk had won nine and lost only one match which made them leading the Croatian Championship with eight points advantage ahead of second ranking Dinamo Zagreb. The management board of Hajduk Split decided to fire Bonačić and promoted Ivić to head coach. After two months, Hajduk had lost many points under Ivić and the management sacked him and asked Bonačić to return. Bonačić returned, but due to the points lost under Ivić, he could only manage a respectable second behind Dinamo Zagreb. Bonačić is known as coach who doesn't like officials of clubs to decide which player will be in the starting eleven. On a few occasions he has left Croatian and foreign clubs when some presidents of clubs have tried to impose him which players "must" play in the first team. In 2006, he was attacked by a group of people whilst returning to his flat in Split. Bonačić claimed that agents of players which were only substitute during his stay at Hajduk because he thought that their quality was not enough good were behind the attack. A few months after this incident he has decided to leave Hajduk and he has told for Croatian press that he will never more return to Hajduk. In 2006, Bonačić accepted an offer as head-coach of Iranian side Sepahan. He was highly successful with Sepahan winning the Hazfi Cup in 2006 and 2007. Also in 2007, he managed to take Sepahan to the AFC Champions League final but lost to Japanese side Urawa Red Diamonds 3–1 on aggregate. Sepahan became the first Iranian football club to make it to the knockout stage and final since Esteghlal in 1990's. In January 2008, Bonačić signed an 18-month contract with Al-Nasr in Dubai and was sacked on February 2009. In December 2010, Bonačić signed a contract with Azadegan League club Gostaresh based in Iran, Tabriz. He returned to his previous club and was named as new head coach of Sepahan on 22 June 2011. After a 3–0 defeat to Mes Kerman in the Pro League and elimination from Champions League, Bonačić was dismissed by club chairman. In September 2012, Bonačić took over the helm of NK Zagreb and headed this team until October 2012 when he was replaced by Miroslav Blažević. On 27 December 2012, Bonačić joined Mes Kerman as head coach for the second time but left the team at the end of the season after leading the club at the sixth place. On 1 July 2013, he was named as the head coach of Zob Ahan, signed a one-year contract with the club. On 16 December 2013, it was announced that Luka will leave Zob Ahan in January 2014 and will be succeeded by Mojtaba Taghavi. On 23 January 2014, Luka returns as manager of Mes Kerman with signing a contract until the end of the season. He led Mes Kerman to the Hazfi Cup finalfor the first time, however, his side lost the match 1–0 to Tractor Sazi. On 6 April, Mes Kerman relegated to the Azadegan League after a 0–0 draw with Saba Qom. He was given a one-year contract by the club to lead them in Azadegan League and promotion back Mes Kerman to the Iran Pro League at the end of the season. However, he was sacked on 11 November 2014 after poor results. On 21 November 2014, he was named as manager of Qatar Stars League side Al-Shahania. On 9 October 2019, Bonačić was named the new head coach of Varaždin in the Croatian First Football League. In June 2020, Bonačić was re-appointed head coach of Iranian club Zob Ahan following the departure of Montenegrin coach Miodrag Radulović.
