Harwich were without Joe Knight so Louie Bloom led their attack, supported by wingmen Zac Pedro and Tiwa Odufuye.
The Shrimpers made a lively start and enjoyed more of the attacking play in the first 15 minutes.
Midway through the half, Benfleet pressed but Harwich defended well and came back strongly with Oakley McNair's header going just over the crossbar and Pedro having a low shot pushed out by goalkeeper Florent Gislette.
The Shrimpers were showing great energy and finding each other with accurate passing movements against a strong Benfleet team who, on their own ground, have pulled off notable victories against the league's leading promotion contenders.
Harwich took the lead in the 54th minute when the referee played the advantage rule when Bloom was fouled but managed to play the ball to Alfie Canning whose pass found Pedro (pictured) in space and the Shrimpers' flying winger burst through to net with a well-placed shot into the corner of the net.
Shrimpers captain Canning was a dynamo in midfield, whilst Pedro was having his best game in a Harwich shirt, causing the home defence major problems.
After a run of 4 straight defeats, 3 by the odd goal, this was a heartening showing by Harwich, who were playing their best football and looked like adding to their lead.
With 75 minutes gone, Benfleet played their part, showing why they have enjoyed success, and with a lightning move down their right flank put Harwich under goal-line pressure. In the ensuing scrimmage, despite strong Harwich protests, the referee awarded a penalty, from which Taylor Lawrence converted Benfleet's equaliser.
Both teams then searched for a winning goal in a nail-biting finish.
A crowd of 201 applauded Benfleet off for their efforts, a testament to how hard Harwich had pushed them, and the Shrimpers' travelling supporters also showed their appreciation for their team's sterling showing.
Harwich team: Brad Cook, Jack Cosby, Charlie Canham, Jack Wood, Reece Harte, Jenson Goode, Oakley McNair, Alfie Canning, Zac Pedro, Tiwa Odufuye and Louie Bloom. Substitutes: Liam White, Mo Hashemi, Jeremiah Ajisafe and Luke Hopwood (all used).