The shock third-round victory was made all the sweeter for Boro considering they had suffered a heartbreaking last-gasp defeat to their hosts in last season’s fourth-round meeting.
Charles had been on target in January last year as a Shane Long goal eliminated the Broadhall Way outfit, but he made his first-half goal count almost a year later to eliminate a toothless Reading side as the former Brentford striker shrugged off his marker to clip beyond Adam Federici’s reach.
A gilt-edged chance went begging in the 58th minute, Simon Church heading the ball into the path of the onrushing Michail Antonio, who sliced wide with only Chris Day to beat.
Reading poured forward as they searched for the goal to keep their FA Cup dream alive, but Manset spurned an easy chance to grab an equaliser four minutes into injury time.
Stoke could face a battle to keep Xherdan Shaqiri as reports have claimed Mark Hughes wants him at Southampton next season.
Bayern Munich have entered the race to Emre Can, who continues to talk up a move away from Liverpool this summer.