Lee Tomlin and Albert Adomah put the visitors two goals up before Gordon Greer halved the deficit late on, and Karanka has said that he was particularly pleased with his side's organisation throughout the 90 minutes.
"It's very pleasing to get three points from this tough game," Karanka told Sky Sports News. "In this league you have to work 100% and today was a good example.
"It's difficult to win games in this league and more difficult to win them away from home. Brighton are a very good team with a very good stadium and they are in a false position. I'm sure they will be climbing the table in the future.
"The team is gelling well as a unit and we kept good organisation. I was pleased with the way we started and the way we went into the second half."
The win has pushed Boro up to third place in the Championship table, one point adrift of leaders Watford.