The 36-year-old midfielder made his last professional appearance when coming on as a late substitute for Nottingham Forest against Brighton & Hove Albion in May 2014.
Last season he played for Tadcaster Albion but has agreed non-contract terms with York where he is a coach.
"With a number of key midfielders out of action, Jonathan will bring experience to the side which could prove vital for us," said new Bootham Crescent boss Jackie McNamara.