The LCR Honda MotoGP rider, currently sixth in the MotoGP standings, came home in one minute 56.500 seconds in Brno ahead of reigning world champion Jorge Lorenzo on his Yamaha Factory Racing bike.
Lorenzo had been in front all day after clocking the fastest lap during first practice in one minute 56.698s but was pipped by German Bradl in the afternoon session despite setting a faster lap time of 1min 56.538s.
Valentino Rossi on his Yamaha was sandwiched between Repsol Honda Team's Dani Pedrosa - who trailed Lorenzo by only a further six hundredths of a second - and current championship leader and team-mate Marc Marquez in fourth.
British duo Cal Crutchlow and Bradley Smith came home sixth and seventh fastest respectively for Monster Yamaha Tech 3.
Completing the top 10 were Spain's Alvaro Bautista on his GO&FUN Honda Gresini and Ducati Team partners Andrea Dovizioso and Nicky Hayden.
Despite topping the times, Bradl admitted he was not entirely satisfied with his bike.
He told motogp.com: "It's nice to be first on Friday but, to be honest, it looks a bit better on paper than it does in reality.
"I am not really super happy with this first position today because we are still missing some confidence with the front of the bike - the front fork is not working as well as I would like.
"The times are really close together and it won't be easy for us tomorrow."
Gresini's Bryan Staring lost control of his bike in the morning session and will be aiming to better his time of 2m 01.746s during Saturday's final practice.