Long bagged the only goal of the game early on to stun Chris Powell's table-toppers.
In the 12th minute Long collected a short pass from Michael Bostwick before crashing home from 20 yards.
Charlton almost levelled when Chris Day produced an excellent stop to deny Dale Stephens.
Long almost doubled his tally when he saw a powerful drive beaten away by Ben Hamer, while at the other end Rhoys Wiggins hammered a shot inches past the post seconds before the half-time whistle.
After the break Jon Ashton came close to doubling Sevenage's advantage, before the Addicks struck back almost immediately when Leon Cort saw a powerful drive well saved by Day as Boro claimed a shock win.