Craig Levein’s side still have an outside chance of making the playoffs, and bounced back from the disappointment of being pegged back in the last minute against Czech Republic on Saturday by getting three points on Tuesday night.
Rangers midfielder Steven Naismith got the winner after 50 minutes, sparing captain Darren Fletcher, who missed a penalty in the first half.
Without the likes of Scott Brown, Kenny Miller and Charlie Adam, Levein will happy with the result, and his side have an outside chance of making the playoffs.
Scotland still have away fixtures against Liechenstein and Spain to play, and realistically need to win both to stand a chance.
Northern Ireland meanwhile were not as lucky, as a poor performance will have disappointed away fans in a 4-1 defeat in Tallinn.
Two goals in each half by the home side secured the victory for the Eastern Europeans, with Nigel Worthington’s men’s only ray of light an own goal in the first half to give them hope.
The side from Windsor Park are now playing for pride in their remaining games, as they host their conquerors Estonia in their next game, before travelling to take on Italy in October.