The home side were made to pay for some early missed chances after 30 minutes when visiting skipper Scott Kerr released Hughton and the 20-year-old fired across Jake Cole to grab the lead.
Lincoln needed an incredible double save from keeper Robert Burch in the 35th minute to keep their lead intact - the former Spurs stopper denying Albert Adomah and John O'Flynn.
Barnet should have equalised in the 62nd minute but Micah Hyde somehow headed a Ryan O'Neil cross over only for Yakubu's header to level proceedings 15 minutes from time.
But John-Lewis had the final say, heading home Joe Anderson's cross to secure Lincoln's third away win this season.
Source: Team Talk
Source: Team Talk