Haunted by defensive errors and low on confidence, the Brewers surrendered all too easily as buoyant Stevenage lifted themselves into the promotion play-off places.
Clough unveiled two new signings - defender Barry Miller from Leigh and midfielder Kris Taylor on loan from Walsall - but they failed to have the desired effect as Borough took control after an even opening 20 minutes.
Anthony Elding was a constant threat, forcing Dan Crane into full-length saves with a shot from the edge of the area and a far-post header.
Burton finally yielded to growing pressure in the 36th minute when they were outwitted by Justin Gregory, who then deftly laid the ball into space for fellow midfielder Simon Weatherstone to crash home a shot from the edge of the area.
Stevenage doubled their lead on the stroke of half-time as Miller's debut was marred by a stroke of rotten luck.
The defender's clearance struck team-mate Ryan Austin on the back and fell kindly for Gregory to pull the ball back into the area where the unmarked Dino Maamria was able to stroke the ball into the empty net.
Burton created little in the way of goalscoring chances themselves and it was symptomatic of a lacklustre performance that the nearest they came to a goal was when a sliced clearance by Boro defender Rob Quinn forced Andy Woodman to make his only taxing save of the game in the 54th minute.
By now, Borough were content to sit back and protect their lead, but Burton's invitation for them to break forward and score a third goal was too good to refuse.
Home skipper Aaron Webster's pass out of defence was intercepted by Weatherstone, who slipped an inch-perfect pass through for Elding to smash home the goal he deserved from 15 yards.
It could have been worse for Burton in the final minute but, with the goal at his mercy, Boro substitute Jermaine Hunter lashed a left-foot shot against the crossbar.