Hubnik had a year remaining on his contract with Hertha, but was allowed to leave before the transfer window closed after failing to establish himself as a regular of late.
The 29-year-old has linked up with Plzen on a 12-month deal and could now face Bayern Munich, Manchester City and CSKA Moscow in the Champions League.
"My family and I have fallen in love with Germany, however the sporting challenge of the Champions League and the fight for the Czech title was too good to turn down," said the centre-back.
"I know I will have to fight for my place as we have three central defenders of high quality, but I want to help the club.
"I am really looking forward to returning to the Czech Republic."
Plzen's general manager Adolf Sadek added: "There is a tight programme ahead of us in the coming days and weeks, so we decided to reinforce our central defence with an experienced defender who can start playing immediately."
Meanwhile, after letting Hubnik leave, Hertha bolstered their squad before Monday's deadline by signing midfielder Tolga Cigerci on loan from Wolfsburg.
Hertha general manager Michael Preetz told the club's official website: "We are happy to have signed Tolga. He is a flexible player for midfield and, except for the holding role, he can play in every position in midfield."