Despite registering more shots on target than their hosts, including hitting the woodwork on three occasions, Birmingham were unable to take a lead back to St Andrews ahead of the second leg on Thursday, August 25.
"[C.D. Nacional] are a quality team, and in Europe to get a draw away from home is a good result," Hughton told the club’s official website.
"Apart from the woodwork we would have won.
"Nacional were good on the counter and we had to work hard but we had the better clear-cut chances."
Birmingham are back in league action this weekend when they travel to Watford on Sunday afternoon.