The 20-year-old striker, signed from Southend last July for £175,000, took his tally to eleven with another impressive performance which destroyed Walsall's hopes of making progress.
Walsall suffered their fifth defeat in nine games to highlight the problems that are now beginning to emerge at the Midlands club.
Their latest reverse was compounded when substitute Ishmel Demontagnac was sent off for an off the ball incident only eight minutes after replacing Troy Deeney.
The gate of 2,318 was Walsall's smallest of the season and the die-hard fans who did turn up were provided with another frustrating performance.
Scunthorpe, beaten only once in their previous 16 games, were also off the boil in the early stages. But it could have been a different story if Paul Hayes had accepted a gilt-edged chance after only nine minutes.
However he laid the ball across to his fellow striker Hooper, who saw his shot saved by the Walsall keeper.
It proved to be an expensive miss as Walsall took an unexpected 24th minute lead. Anthony Gerrard's cross was deflected into the path of Paul Ricketts who scored with a subtle lobbed shot.
But the League One leaders slowly worked their way back into contention against a badly disjointed side.
Martyn Woolford was a clever midfield worker and slowly Scunthorpe applied a lot of pressure on the suspect defence in which Stephen Roberts was often ill at ease against the duel-pronged attack of Hayes and Hooper.
An equaliser was always on the cards as Walsall were relentlessly pushed further and further back onto the defensive.
Walsall finally capitulated three minutes before half-time when Cliff Byrne slipped a low ball into the path of Hooper who scored with a low drive beating the Walsall goalkeeper at his near post.
Exploiting the gaps in Walsall's sagging defence it was hardly a surprise that Hooper notched his second on the scoresheet in 58th minute.
He again created space for himself to receive Woolford's pass and scored his eleventh goal of the season with another accurate low cross shot into the corner of the net.
United played some exhilarating second half football and Hooper thought he had finished off his hat trick when he smashed in a contender for goal of the season, a vicious volley on the turn from 25 yards, only to see the linesman's flag up for offside.
But the tie was sealed when Walsall's Ishmael Demontagnac, a second half substitute who was ironically cheered onto the field was sent off for raising his hands at Lea, which was well spotted by the linesman.
Facing 10 men Scunthorpe, sealed the match when Kevan Hurst collected a clearance from Joe Murphy and cut inside to unleash a terrific strike that found the top corner.
Hurst, who has been out the side for a long spell will be boosted by the goal, and he celebrated infront of United's 400 strong contingent.
