Donovan Wilson netted the only goal of the match as the Yellow Army took won their third straight contest at home without conceding a goal and have lost just three times at the VBS all season.
The Sulphurites have dropped four consecutive matches and sit tenth after being as high as second earlier in the season.
Story of the match
On the half-hour, Sutton found the eventual match-winner when Omar Bugiel slipped the ball past two Sulphurites defenders and into the path of Wilson, who finished low past Mark Oxley.
The visitors came close to an equalizer when Thomson flew his shot over the bar in a first half that saw few chances.
Harrogate began the second half on the front foot, Thomson sending a ball into the Sutton box that was dealt with before Warren Burrell shot wide from the edge of the area.
Thomson was again at the heart of a Harrogate chance as his pass found Alex Pattison, whose near-post effort was well-served by Dean Bouzanis.
In the 62nd minute, the Sutton goalkeeper was again called into action as he stopped Hall's header that was set up by a Thomson corner.
The action picked up as both teams threatened. Substitute Jack Muldoon tested Bouzanis and Pattison saw multiple shots blocked, Will Randall volleyed past the upright in between for the hosts.
Bouzanis made the save of the match in the 90th minute after Muldoon had headed Ryan Fallowfield's cross on goal.
Man of the match: Donovan Wilson
He scored for the first time in two months and provides Harrogate with another threat up front, especially if he can replicate his form from last season.