Fillon, who was the overwhelming favourite to win the second round, had taken a big lead after early results, winning 68.7 per cent of early votes while Juppé accounted for just 32 per cent of the votes.
The Les Republicains candidate is widely tipped by pollsters to face far right leader Marine Le Pen – and beat her – in a second round run-off in the presidential election scheduled to be held in May next year. But the race is seen as highly unpredictable because of uncertainty about the impact of independents and the Socialist party candidate.
President François Hollande has yet to announce whether he will try to defy his historically low approval ratings by running for a second term.
A survey on Friday showed current Prime Minister Manuel Valls would be a far more popular candidate than Hollande.
Valls has not ruled himself out of contesting in the left-wing primary set for January, telling the weekly Journal du Dimanche he wanted to dispel the idea “that the left has no chance” of retaining power.
Hollande’s former protege and economy minister, 38-year-old Emmanuel Macron, is also set to stand for the presidency as a centrist independent.