Goals from Hayden Hackney and Rumarn Burrell helped stretch our Under-23s' unbeaten run to three matches having defeated Reading.
Hackney was successful from the penalty spot on nine minutes, but the Royals levelled in the second half through an own goal.
However, Boro made it back-to-back victories in the league - and three games unbeaten in all competitions - when Burrell followed up a rebound.
Hayden Coulson got his first minutes since August - playing just under an hour - after suffering from a thigh injury, and the left back was heavily involved throughout for Graeme Lee's side.
Boro took the lead with just nine minutes played as Djed Spence worked his way into the box and was brought down by a Reading defender. The referee pointed to the spot, and Hackney dispatched the spot kick.
The visitors looked for a swift response to falling behind as Oliver Pendlebury tried his luck from distance, but his effort was way off target.
The Royals carved out another opening on 20 minutes when Thierry Nevers dispossessed a Boro man, but he sent an attempt on goal way over the top of the bar.
Adam Liddle came close with a couple of chances in the closing minutes of the first half for the visitors, as he looked to convert a low cross, only to be denied by a vital block, and he tested Sol Brynn from just outside the box in first half stoppage time but it was straight into his gloves.
Coulson almost added his name to the scoresheet on 54 minutes, as he swept across a low drive from a narrow angle.
Reading were back on terms with just under an hour gone as Nevers fed Liddle, whose shot took a deflection and Jack Robinson couldn't prevent it from rolling into the bottom corner.
Liddle came close to putting the Royals in front for the first time when a powerful header was well saved, and Boro also pressed for a goal to restore the advantage, but Paddy Reading's low delivery flashed across the box untouched.
However, Boro re-established the lead with just over 15 minutes remaining as Stephen Wearne saw his low shot saved by the Reading stopper Coniah Boyce-Clarke, and Burrell tapped home the rebound.
The lead for the Teessiders was almost two when Wearne connected with Reading's cross, but his header was saved by the Royals stopper.
Boro: Brynn, Dodds, Dale (capt), Hood, Robinson, Spence (Jones 63), Wearne, Hackney, Coulson (57), Folarin (Walker 46), Burrell. Unused subs: Hemming
Reading: Boyce-Clarke, Elva-Fountaine, Medforth-Smith, Pendlebury, Nditi, Osho (capt), Azeez (Bristow 63), Caetano, Liddle, Lawless (Nolan 57), Nevers (Beedan 80). Unused subs:Andresson