Bradley Fewster gave Boro a ninth-minute lead from close-range, but Joseph Mendes superbly converted Ryan East’s perfectly timed ball over the top for a first-half leveller.
Gabriel Osho (pictured above) headed in from a corner shortly after the interval, before Mendes added a second and Yakou Meite volleyed in their fourth late on.
The quarter-final draw for the PL Cup will take place live on twitter.com/PLYouth from 12pm on Tuesday 21 March.
Reading’s next Premier League 2 match is at home to Arsenal on Monday 10 April, while Middlesbrough visit West Ham United at the London Stadium on the next day.
See: Middlesbrough report