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Reading chalked up their first away win in the First Division and were indebted to the finishing skill of Hughes.
The former Notts County player linked with John Salako to notch his two goals to destroy Walsall.
Hughes had previously failed to score this season but after getting the first took obvious delight in sealing the match with his late strike.
Walsall, following two successive wins, had nothing but disappointment as they had Roberto Martinez sent off for two bookings late in the game.
But there was an early indication of the way the game would end as early as the first minute.
The Saddlers very nearly made a sensational start with a goal from Jorge Leitao but his effort after just 25 seconds was ruled offside.
Reading, fresh from their conclusive win over Burnley, were accorded few opportunities to make an impact as an attacking unit in the first half.
Walsall's defence was secure with the big central defender Danny Hay making an important contribution.
The most anxious moment for Walsall came from a powerful low free-kick from Jamie Cureton. Walsall's goalkeeper and acting skipper, James Walker, had to make a diving save when he had little time to spot the ball coming through the wall.
Walker's clean handling was a feature of the game and did much to keep the Saddlers in the match.
In sharp contrast Marcus Hahnemann, who had a trial with Walsall during the summer, had a quiet time in Reading's goal in the first period.
Hahnemann later saved well from Leitao and Gary Birch as Walsall stepped up the pace.
In the closing stages Walsall drafted in striker Junior in place of Steve Corica.
The Brazilian was only granted international clearance hours before the game and made a pleasing first appearance but even he could not open up the Royals defence in which John Mackie and Adie Williams were the king-pins.
Hughes then played a return pass with Salako for his first goal and the two repeated the act in the last minute