Although, with a little more fortune they might easily have been celebrating a victory.
Blues, competing in a major European competition for the first time since 1962, struck the woodwork three times at the Estadio da Madeira but in the end had to settle for a draw.
Nevertheless, Hughton was pleased with that, saying: "I'm very happy with the result. We played at a special stadium against a good team. Of course to get a draw away in a competition like this is always good."
Chris Wood was twice denied by the frame of the goal in a five-minute spell either side of half-time while Steven Caldwell also saw a first-half header strike the post as Blues came closest to breaking the deadlock.
"Nacional were strong going forward and that made us work a lot, but the better goalscoring chances belonged to us and we could have won here," Hughton continued.
"Nacional started better and trailing at the beginning of a game is always bad. That didn't happen and with time we improved and got a better performance."
Nacional coach Ivo Vieira was disappointed at not being able to gain an advantage ahead of the trip to St Andrew's, saying: "It's a negative result for us as we wanted to win to get some comfort to travel to England.
"Despite the Birmingham shots that hit the posts, the game was balanced.
"We knew it would be a tough game, but even so we created some goal chances. We knew Birmingham are a very competitive opponent and the fact they play in the Championship means nothing as they have a budget superior to all the clubs of the Portuguese top flight, excluding the three big clubs (Porto, Benfica and Sporting Lisbon).
"We tried hard, but the goal didn't arrive. If we get a goal in Birmingham we can cause problems for our opponents and that's what we are going to look for there."