Grimsby made the trip to the capital having triumphed in the same venue over Forest Green Rovers seven days ago to secure their return to the Football League.
Clear openings were at a premium during the first half, with neither goalkeeper called into any meaningful action.
Yet, that changed just three minutes after the restart when McManus struck to clinch the trophy for the Shaymen on their first ever visit to the home of English football.
The former Manchester United trainee tried his luck with a left-footed curler from 25 yards and he was rewarded as the ball flew into the top corner of the net.
Deep into stoppage time Grimsby's leading goalscorer Padraig Amond had the chance to level up the score, but his shot from close range was hacked off the line.