As a player, Komňacký played for regional clubs from South Moravia, his native region. In 1970 he went to Russia to study pedagogy and played four years until his graduation for Neftyanik Volgograd. After his return he played again for regional teams but in 1978 also began his managerial career, he then led the youth team of Jiskra Kyjov.
His first work as a head manager was at FK Drnovice in 1986-1988, he then coached Hanácká Slavia Kroměříž and Tatran Poštorná.
In 1997 he began work at 1. FC Synot and advanced with the team to the Gambrinus liga. He then led FK Zlín and MŠK Žilina. In the 2002-2003 season Komňacký led Matador Púchov and won the Slovak Cup with them. For the next season he returned to the Czech Republic to work at Silesian club FC Baník Ostrava.
Baník led the league almost the whole 2003-2004 season and won the Gambrinus liga for the first time in the history of the independent Czech Republic. Six years later Komňacký remembered that season: "I spent there a wonderful season, which I will not forget. I have that club and region in my heart."
Afterwards Komňacký went back to Slovakia and won both the Slovak Cup and the Corgoň Liga with MFK Ružomberok in the 2005-2006 season. He recently said that winning a double with MFK Ružomberok was his biggest success so far in his manager career. Since October 2007 he has coached FK Jablonec. In the 2009-2010 season, Jablonec finished second in the Gambrinus liga for the first time in its history.
He received several awards for his achievements. In 2004 he was awarded the Rudolf Vytlačil Award for the Czech Coach of the Year, for leading FC Baník Ostrava to the national championship. In 2009 he was awarded the Czech Coach of the Year award for a progress he made with FK Jablonec. In 2010 he was again awarded the Rudolf Vytlačil Award for the Czech Coach of the Year, for leading FK Jablonec to the historic success of runner-up position in the 2009-2010 season.
In January 2010 he signed a contract extension to keep him at Jablonec until the end of June 2011.