The Belgian mastered the gruelling Greek roads to finish ahead of fellow Hyundai drivers Dani Sordo and Ott Tanak respectively.
Ogier, Neuville’s nearest title challenger, dropped out of third place overnight after his crash.
Neuville had led since midday Saturday and unlike his rivals avoided trouble on the punishing roads on the final day to achieve his second success of the season after the opening round in Monte-Carlo.
“We followed our objectives throughout the weekend and it paid off. The car worked perfectly so I have to thank the team,” Neuville said after his 21st WRC success.
“I didn’t have the information on Ogier’s crash at all, and when I saw the car I still wasn’t sure it was him.
“I understood from that point on that I just had to bring home the car and get through.”
The Belgian had approached the Acropolis Rally under pressure, with Ogier just 27 points behind.