The Seagulls looked set for a goalless draw until the 86th minute when Matthew Upson's header from a corner snatched victory.
Jones said: "Every win is a big win in this division but to come to Middlesbrough and win is a very good result.
"Believe me, and I'm not being condescending, but they are in a false position. They are a good side who should be higher than they are in the table, so it was a massive three points for us.
"And it wasn't easy. We started well in the first 20 minutes but after that we had to grind it out. We weren't fluid and they had a lot of possession in the second half.
"They were playing well but we tried to win it and we made a few positive substitutions, so it was ironic we won it with a set piece.
"It wasn't the way we planned it but we'll take that."