Jean Beausejour had fired Blues into an early lead against the Clarets at St Andrews on Tuesday night but, as they had done against Peterborough on Saturday, Blues failed to stamp their authority on the the game by adding to their goal tally and the visitors looked to have snatched a point when Marvin Harley equalised early in the second half.
However, Blues got their just rewards on this occasion when Chris Burke grabbed a late winner one minute into stoppage time.
"We left it very late but the plus to take from it is the fact there is a lot of spirit in the camp and they are a determined group of players," Hughton said after the 2-1 victory.
"We certainly didn't make life as easy for ourselves as we should have done but I was very happy with some of our offensive play.
"We just need to make sure we start working the opposition goalkeeper more than we are doing at the moment."