A Willie Clemens header gave Bermuda the lead on eight minutes before Jaylon Bather doubled the advantage from close range in the 19th minute.
Barbadian pressure after the break brought dividends when Zeco Edmee pulled a goal back in the 59th minute.
But Bermuda appeared to be heading for victory until Howell replaced captain Mario Harte in the 87th minute, scoring the equaliser a minute later after a blunder by home goalkeeper Quinaceo Hunt.
Howell then stunned home fans by grabbing the winner in the three minutes of added time as the visitors turned the game on its head.
The victory avenged a 3-0 defeat Barbados suffered when they last visited Bermuda almost a decade ago.