McLaren, which leads the current drivers' and constructors' standings, was punished by the World Motor Sports Council for allegedly using leaked secret technical documents belonging to F1 rival Ferrari.
The team can appeal.
Rookie English driver Hamilton leads the standings with 92 points, followed by two-time F1 champion Alonso of Spain with 89.
Ferrari teammates Kimi Raikkonen (74) and Felipe Massa (69) are third and fourth.
Four races remain in the season, starting with Sunday's Belgian Grand Prix.
Hamilton and Alonso finished 1-2 in Sunday's Italian Grand Prix, at Ferrari's home track of Monza, to extend McLaren's lead in the constructors' championship to 23 points.
Prior to the sanction McLaren had 166 points, Ferrari 143.