Simon Cox struck in the seventh minute as the Royals ultimately grabbed their second league win of the season.
Karanka was left bemoaning the events thereafter, with apparent Reading time-wasting going unpunished as his side failed to grab what would have been a deserved leveller.
He said: “It is something that I do not like (time-wasting).
“It is frustrating but they can do it. Me and a member of my staff went to the linesman and fourth official and they didn’t want to speak with us.
“Then 30 seconds later they were with the other bench laughing and joking. That is what is frustrating, not Reading’s game.
“I am frustrated by the fourth official’s behaviour and it is not the first time. We were playing at the tempo the referee wanted. He wanted to stop play and he did.
“If the goalkeeper wanted to keep the ball for 13 seconds before a goal kick, they let it happen.”
Opposite number Nigel Adkins remained tight-lipped when asked for a response, saying: “Time-wasting tactics? I don’t want to get involved in any of that. I thought it was an excellent 1-0 victory.”
That Reading won with a severely depleted squad unsurprisingly brought great satisfaction for the manager. Adkins added: “We had 16 players unavailable going into the game so it’s a great result. It was a super goal from Simon Cox.”
Middlesbrough: Mejias, Damia, Hines (Luke Williams 76), Omeruo, Friend, Clayton (Whitehead 77), Leadbitter, Adomah, Tomlin (Bamford 59), Reach, Garcia. Unused substitutes: Ayala, Gibson, Ledesma, Konstantopoulos.
Reading: Federici, Gunter, Hector, Pearce, Obita, Edwards, Kuhl (Akpan 53), Norwood (Cooper 82), Taylor, Cox (Tanner 56), Mackie. Unused substitutes: Andersen, Long, Stacey, Fosu.
Referee: D Bond (Lancashire).
Man of the match: Alex Pearce.