An 80th minute header from substitute Ayo Akinsete - who had been on the pitch for just five minutes - grabbed victory for Tony Carr's team in an even match that could have gone either way.
After Arsenal had seen a goal disallowed for offside, an excellent move involving Phil Lumsden and Greg Pearson ended with Daryl McMahon sending over a superb deep cross that was headed in at the far post by Akinsete.
Said Tony afterwards: "After last week's defeat against Ipswich, it was important to get back to winning ways and the players deserve credit for bouncing back against a very good Arsenal side.
"The game was very nip and tuck, with not much between the two teams, and it could have gone either way.
"It was looking likely that the game would end up as a draw, but our goal rounded off a fantastic move and we held firm for the last 10 minutes without Arsenal causing us too many problems."
Team: Jackson, Khan, Tattam, Johnson, Ward, Lumsden, Allen, McMahon, Mehmet (Carrick 75), Eastwood (Pearson 60), Cole (Akinsete 75).
Meanwhile, a goal from defender Liam Parrington wasn't enough to secure victory for the under-17s against Reading in a game played at Upton Park as a prelude to the live beamback of our Premiership clash at Chelsea in the afternoon.
The hosts took the lead midway through the second half when Parrington header home a corner, but the visitors equalised with just five minutes remaining to earn a share of the points.
Said Kevin Keen afterwards: "It was a rather disappointing performance from the players and I think they may have been a little overawed by the occasion.
"There was a touch of nervousness in our play and I think Reading maybe coped better with the situation than we did.
"Saying that, it was a fantastic experience for the boys, one they will learn from, and the important thing is that we didn't lose. We are now four games unbeaten and it is a habit I want the players to get used to."
Team: Reed, Wright, Cohen, Parrington, Laws, Blewitt, Tucker, Noble (Singh 89), Bunce, Lee (Lee 60), Collington. Subs unused: Behcet, Henry, Stokes.