Johjima will not be permitted to throw for the next eight weeks, meaning that his season has effectively ended for 2011.
The 35-year-old had initially said he would not go under the knife, but he was later convinced to have the surgery at an Osaka hospital after talks with Hanshin manager Akinobu Mayumi.
''Now that I have undergone surgery, I want to do my best to return as catcher as soon as possible,'' Johjima said in a statement.
Johjima had surgery on the same knee during the 2010 offseason.
This season, he was forced to leave the team in June due to the injuries after playing 38 games and hitting just .189 with five home runs and 13 RBIs.