The Bayview club lost their relegation play-off 3-2 to Stirling Albion, a miserable end to a campaign which saw the club win just four regular season matches following Naysmith's appointment in December. But chairman Lee Murray has given the manager his full backing.
"I gave Gary an 18-month contract in December and we have a two-year plan for building this club," he said. "His job is certainly safe as far as I'm concerned.
"The difference from the start of the season to now is unbelievable."