Reading scored two first-half goals in the space of eight minutes through Michael Morrison and Ovie Ejaria, before Garath McCleary came off the bench to score their third with just over ten minutes to go.
The fourth successive defeat means Town remain a place above the relegation zone as they now go into the two-week international break.
With four changes to the team that lost to Nottingham Forest the previous week, including Lloyd Jones coming in for Sonny Bradley for his first league start for the Town, the Hatters started the game on top and had the best chance of the opening exchanges, which fell to captain for the afternoon Martin Cranie.
After Harry Cornick won a free-kick on the right, Jacob Butterfield delivered and the ball found its way to Cranie at the back post, who took a touch out of his feet before firing a left-footed effort on goal which Rafael was able to beat away.
Town were again pushing forward early in the game as Butterfield turned defence into attack with a lofted ball out wide for Cornick. From there, the winger progressed forward before crossing deep for Collins, who headed wide on the stretch, although referee Andy Woolmer penalised the striker for a foul.
Reading then created chances of their own and took advantage. Omar Richards wiggled his way into the box and fired a right-footed shot on goal, which Shea did well to turn behind.
But from the resulting corner, Reading took the lead through Morrison’s second goal of the season as he headed John Swift’s corner beyond Shea's reach into the top corner.
The hosts then doubled their lead on the half-hour mark as Ejaria curled the ball in from the edge of the box. After receiving the ball out wide on the left, he made space to unleash a shot and his effort found the bottom corner with the aid of a deflection.
The intensity petered out in the second half until the 68th minute, when Puscas brought a fine save out of Shea.
Town tried to get back into the game and had a handball claim turned down with 15 minutes to play. Second-half substitute Alan Sheehan’s corner was whipped in to the six-yard box and as several players challenged for a header, everyone in an orange shirt appealed for a penalty, but referee Andy Woolmer was unmoved.
Shortly after, in the 79th minute, Reading wrapped up the three points as substitute Garath McCleary won the ball from Sheehan and raced forward to finish calmly past Shea.
The win was Reading’s third consecutive home victory under Mark Bowen as they remain unbeaten since he took over. They push up to 17th, while the Hatters stay in 21st place with Leeds United up next at Kenilworth Road in a fortnight's time.
TOWN: Shea, Bolton (Sheehan 45), Cranie (C), Jones, Pearson, Potts, Tunnicliffe, Butterfield (LuaLua 69), McManaman, Cornick (Shinnie 58), Collins. Subs not used: Sluga, Lee, Mpanzu, Bree.
Yellows: Bolton
READING: Rafael, Morrison, Miazga, Moore (C), Yiadom, Swift, Ejaria (McCleary 64), Rinomhota, Richards, Baldock (Loader 80), Puscas (Meite 69). Subs not used: Walker, Loader, Howe, Blackett, Pele.
Goals: Morrison (22) Ejaria (30) McCleary (79)
Referee: Andy Woolmer
Attendance: 15,251 (2,097 Hatters)