Howell's 89th minute strike from the edge of the area smashed into the unlucky Andrew Whing before looping over Clarke via a deflection off Howell's knee.
Gary Waddock's visitors were forced into a change before kick-off when Alfie Potter, originally named in the starting line-up, suffered a groin injury during the warm up with Ryan Williams replacing the United front man.
Despite a quiet opening 45 minutes for both goalkeepers it was Williams who squandered the best opportunity of the half. The midfielder, on loan from Fulham, sent Josh Ruffels scampering down the right. The winger's cut back found Williams who could only blaze over the crossbar from 12 yards when well placed.
Second-half substitute James Constable saw a powerful shot saved by Chris Lewington's legs, before smashing a shot just past the far post late on.