The 29-year-old, a bronze medallist in Zagreb in 2013, led Russian duo Dmitri Aliev and Artur Danielian.
Skating to "Baby Did a Bad Bad Thing" by Chris Isaac, Brezina produced a quadruple Salchow-double toeloop, a triple flip and triple Axel for a score of 89.77 points.
"It's my 13th Europeans, so it only took 13 years. I practiced well, and I just did what I do at practices for the past one and a half months," he said.
Danielian, at 16 the youngest man in the competition, performed a flamenco routine with a quadruple Salchow and triple Lutz-triple toe as well as difficult spins and footwork, but he stumbled on the triple Axel.
The 2018 world junior silver medallist set a new personal best of 84.63 points.
1. Michal Brezina (CZE) 89.77 points, 2. Dmitri Aliev (RUS) 88.45, 3. Artur Danielian (RUS) 84.63, 4. Morisi Kvitelashvili (GEO) 82.77, 5. Deniss Vasiljevs (LAT) 80.44, 6. Paul Fentz (GER) 80.41, 7. Matteo Rizzo (ITA) 79.07, 8. Alexei Bychenko (ISR) 78.27, 9. Aleksandr Selevko (EST) 77.45, 10. Gabriele Frangipani (ITA) 76.91
1. Aleksandra Boikova/Dmitrii Kozlovskii (RUS) 82.34 points, 2. Daria Pavliuchenko/Denis Khodykin (RUS) 74.92, 3. Evgenia Tarasova / Vladimir Morozov (RUS) 73.50, 4. Nicole Della Monica/Matteo Guarise (ITA) 70.48, 5. Minerva Fabienne Hase/ Nolan Seegert (GER) 70.43, 6. Miriam Ziegler/Severin Kiefer (AUT) 67.90, 7. Annika Hocke/Robert Kunkel (GER) 58.43, 8. Rebecca Ghilardi/Filippo Ambrosini (ITA) 56.85, 9. Coline Keriven/Noël-Antoine Pierre (FRA) 51.47, 10. Ioulia Chtchetinina/Mark Magyar (HUN) 51.03