Joe Martin - playing at left back - netted the only goal to maintain Gillingham's 100% record, converting Myles Weston's 30-yard free-kick which had rebounded off the post.
"What a magic second-half, that was a fantastic second-half performance from the players," said Allen.
"To see them once again celebrating in front of our travelling support that sung their hearts out from start to finish behind that goal is great.
"It was always going to be hard here, they almost beat Watford last week in the cup so we knew it was going to be tough.
"I thought we did ok in the first-half, but in the second we went up another level with pace and power - we lifted our game completely and thoroughly deserved to win."