Boro have now won five out of their last six in the Sky Bet Championship and have kept five clean sheets along the way in a marked upturn in form.
They sealed victory at the Riverside with a long-range effort from Emmanuel Ledesma in the 16th minute but were left hanging on nervously in a frantic finale.
Karanka said: "I was very happy when the final whistle went because I was really suffering there at the end.
"It was another three points and another clean sheet so I must be satisfied - but it was not a good game.
"We did not play as well as we can or as well as we should so I was not happy at that. We did not move the ball quickly enough and we did not press our advantage when we were on top of the game.
"But it was a game that we may have lost in the past and it is another win so that is a good thing.
"And it is a big lesson for us. It has showed how difficult it is to win games in the Championship, how hard you must work to get in front and how hard it is to stay there."
Charlton boss Chris Powell was unhappy at some key decisions that went against his side.
They had what looked a good goal by Simon Church ruled out for a foul in an aerial challenge with Boro keeper Shay Given and then soon after were down to 10 men after Rhoys Wiggins was shown a straight red card in the 84th minute.
"We started off showing Middlesbrough too much respect but we grew into the game," he said.
"But things are going against us in games at the moment.
"Simon's was definitely a goal for me. It was a brave challenge but a fair challenge. There was no danger, no intent and he got there first.
"And Rhoys, well, the ball ran away from him and he tried to get it back. Yes, he caught him but it wasn't two footed, it wasn't off the ground. I thought it was harsh but I haven't decided yet if I will appeal."
Charlton are now just above the drop zone but Powell believes they have the spirit to stay up.
"Things haven't gone well for us but we have to keep battling," he said.
"It will be a tough second half of the season but if we keep showing that spirit then we will give ourselves a fighting chance in every game."