Barnet, whose player-manager is former Champions League winner Edgar Davids, were playing the last game after 106 years at the north London ground with the sloping pitch, and victory took them out of the relegation zone with one match to play.
Instead of the usual gate of around 2,000 fans, more than 6,000 turned up with the kickoff delayed by 15 minutes and they saw Barnet win with a late goal from Jake Hyde, minutes before goalkeeper Graham Stack saved Joel Grant's penalty.
Davids, who won the Champions League with Ajax Amsterdam in 1995 and whose other clubs include Juventus, Inter Milan and Tottenham Hotspur, played 85 minutes of the game and said afterwards: "It was not the ideal scenario, but we won and we still have one match to play.
"If we play with the same intensity and determination I think we can stay in the League."
Barnet are leaving the ground, where Arsenal's development teams play, after a long battle with the local council and are moving to a new ground The Hive, five miles away (eight kilometres) next season.
The final match of the season is at Northampton Town next week and they need a win to stand any chance of avoiding a return to the minor Conference League after their current run of eight seasons in the Football League.