The defeat saw them dropped down one place to 6th on the 24 team table with 42 points from 25 games, a massive 13 points adrift of leaders Oxford United at the summit of the only Blue Square Premier Division automatic promotion spot.
Adam Tann had a shot blocked and Bradley Hudson-Odoi saw the rebound superbly saved by keeper Lee Harper as the home side shaded the first 45 minutes.
But it took almost an hour for the Stutes to break the deadlock, Michael Frew crossing from the right for Tann to slam home from six yards.
The visitors dominated late on, Simon Heslop and Anthony Elding firing wide.
Elding had earlier also had a shot tipped round the post by home keeper Danny Naisbitt.
But Histon withstood Kettering’s late rally to stretch their unbeaten league run to five matches.