In the second event of the Chase for the Sprint Cup, Logano claimed line honours having finished fourth at the MyAFibStory.com 400 at Chicagoland Speedway - a result he was greatly disappointed with.
Logano, who debuted in the race in 2008, claimed the win at the New Hampshire Motor Speedway for the first time, making it four race victories this season to continue his consistent campaign.
The 24-year-old has finished in the top six in eight of the past nine NASCAR races, including two wins and two thirds.
The result took Logano (2096 points) into second in the Sprint Cup Series standings, ahead of Hendrick Motorsports' Jeff Gordon (2070), who finished 26th on Sunday.
A late tyre cut halted Gordon late on in the 303-lap contest, as he finished outside the top-20 for just the fourth time in 2014.
The poor result saw Gordon slip to seventh in the standings, also behind Kevin Harvick (2090), Jimmie Johnson (2080), Kyle Busch (2077) and Dale Earnhardt Jr (2077).
Championship leader Brad Keselowski (2097), Logano's team-mate, held firm in top spot with a seventh-place finish.
Runner-up behind Logano was Kyle Larson (Chip Ganassi Racing), who is not among the Chase for the Sprint Cup participants.
Rounding out the podium was Stewart-Haas Racing's Harvick.
Harvick led for 104 laps on Sunday, before posting his 10th top-five result of the season.