Midfielder Hughes has put pen to paper on a one-and-a-half year extension, so will remain with the club until 2014.
Full-back Naysmith was taken to Pittodrie on a short contract, due to be up in January, but he will now spend the full season with Aberdeen.
Both players are currently injured, but have provided much-needed experience to the Dons' young squad.
Dons boss Craig Brown said: "Both players are happy to be at the club and we are happy to have them."