Ciaron Brown scored twice while Isaac Price added the winning strike, securing three points for Michael O'Neill's side despite an all-round display that fell short of their potential.
The match marked the third and final leg of a demanding four-game tournament cycle in September and October, with the hosts having previously drawn 0-0 against Georgia at the Clearer Twist National Stadium in Windsor Park earlier this week.
Although Northern Ireland created numerous opportunities throughout the contest, they were unable to convert their superior play into additional goals as Georgian goalkeeper Giorgi Mamardashvili made a series of solid saves.
The travelling contingent comprising 700 supporters from Derry and surrounding areas gathered in the stadium to mark the conclusion of the fixture.
In the standings, Northern Ireland sit atop the table with eight points accumulated from four matches, having previously drawn 0-0 with Hungary on Monday.
Hungary occupy second place with seven points, while Ukraine hold fourth with four points and Georgia are bottom of the group with two points.
The next fixtures for the hosts include a trip to Belfast against Ukraine in November and a home match in Budapest against Hungary.
Northern Ireland previously defeated Ukraine 3-0 away from home on Friday night during this same tournament series.
Three substitutions were made by the manager compared to the squad that started the earlier encounter with Ukraine.