Nine-time world rally champion Sebastien Loeb and Spanish driver Cristina Gutierrez finished third in Punta del Este on Sunday to beat inaugural champions Rosberg X Racing by two points in the final standings.
"I'm so proud of the team and these two amazing drivers," seven times F1 champion Hamilton, who takes a close interest in the off-road electric series without competing himself, said on Instagram.
The series, with identical SUVs and male and female drivers in every lineup, launched last year and aims to raise awareness about climate change and promote sustainability by racing in remote and damaged environments.
Rosberg X Racing, with Sweden's Johan Kristoffersson and Mikaela Ahlin-Kottinsky, had been 17 points clear of X44 before the final round.
Rosberg's team beat Hamilton's on a tiebreak last year after finishing level on points.
