In an astonishing finish to a race he had dominated from pole position, the Briton stretched his Formula One world championship lead to 30 points.
Red Bull's Max Verstappen finished second, and would have won had he not pitted for fresh tyres in a bid to score an extra point for the fastest lap, with Ferrari's Charles Leclerc third.
Hamilton's team mate and closest rival Valtteri Bottas failed to score after also suffering a late puncture and finishing 11th. (Reporting by Alan Baldwin, editing by Gareth Jones)
Afternoon Session, Semi-finals
Clermont-Ferrand - Saint-Christo-en-Jarez
MX2 - Race 2, Riga
First Session, Semi-finals
Women's Singles, Day 3
Stage 1, Clermont-Ferrand - Saint-Christo-en-Jarez