The Serb said last week that he was considering going without a coach after ending a five-year partnership with Croatian coach Goran Ivanisevic last month, following his early exit from Indian Wells.
The Italian Panichi joined Djokovic's team as fitness coach in 2017.
"What amazing years of collaboration we’ve had. We reached the summit, won titles, broken records. But most of all, I have enjoyed our most 'ordinary' days of training in and out of the gym," Djokovic wrote on Instagram.
"(Thank you) for all the energy, effort and time you invested in making me the best possible player and person I can be. Much love."
Djokovic skipped the Madrid Open this year to focus on the Grand Slams and the upcoming Paris Olympics, but plans to compete in Rome.