Charlton have agreed to sign Gower on a one-year deal.
"Mark is a player who came in towards the end of last season and, after initially having to wait for his chance, made a real impact in the final few games," said Charlton boss Chris Powell told the club's website.
"He offers us good experience in the middle of the park, is a good user of the ball and has played in the Premier League with Swansea.
"He is a player I have had my eye on for a while, even before he joined us on loan, and he adds to the competition for places in midfield.
"Along with the likes of Andy Hughes, who signed a new contract last week, he is another good character and I'm very glad to have him on board for next season."