Harwich made a great start, taking the lead in the 5th minute with a well-worked goal. Jack Wood's lovely diagonal cross pin-pointed Alfie Canning. He then found Alfie Smith, who was running at goal and he netted with a neat header.
Whitton capitalised on lax marking in the Shrimpers defence to equalise in the 11th minute.
Harwich suffered a blow when, with 15 minutes gone, Joe Knight (pictured) was red-carded following a challenge near the touchline.
With captain Gareth Heath back in the starting line-up and in good form dictating in midfield, 10-man Harwich still had the edge and were looking good.
In a 5-minute spell before half time it seemed that Harwich must score and take the lead. Louie Bloom and Liam Riley both came within inches of netting, Canning had an effort cleared off the line and, in between, the Whitton goalkeeper pulled off an excellent save.
Encouraged by this, Harwich started the second half hopeful that they would defy the numerical odds as they had already done on previous occasions this season.
However, it was Whitton who took the lead from a cross from their right-hand flank that was converted at the far post.
On their sloping pitch, Whitton now fought tigerishly to hold on to their lead by allowing Harwich no space or time on the ball.
Despite determined efforts, it was not until the closing stages that Harwich were able to create any scoring chances. Then Bloom broke through the home defence and his cross only lacked a final touch to end up in the net. Heath sent over a corner kick that beat the Whitton defenders but tantalisingly somehow did not end up in the back of the net either.
Time ran out for Harwich and elsewhere league leaders Haverhill Rovers had managed to come from behind to beat Needham Market Reserves 3-2 and open an 11-point gap at the top, albeit having played two games more than the Shrimpers.
Harwich team: Brad Cook, Alfie Eldridge, Jack Wood, Tyler Sullivan, Reece Harte, Alfie Smith, Gareth Heath (captain), Liam Riley, Louie Bloom, Joe Knight and Alfie Canning. Substitutes: Danny Garrad, Greg Rodger, Liam White, Keelan Milburn (all used) and Dan Keeble (not used).