Fillon, a conservative Catholic strongly opposed to same-sex marriage, positioned himself firmly to Alain Juppé's right.
Both Fillon, 62 and Juppé, 71, knocked their former boss, former President Nicolas Sarkozy, out of primary's first round. Mr Sarkozy then threw his support behind Fillon, who served as his Prime Minister from 2007 to 2012.
Juppé served as French foreign minister and defence minister under Mr Sarkozy and Prime Minister from 1995 to 1997 under President Jacques Chirac.
The two opponents disagreed on the best approach towards Russia with Fillon calling for greater ties with the Kremlin and working alongside President Putin in the fight with Isis.
Fillon insists "Russia poses no threat" to the West, while Juppe wants France to continue putting pressure on Putin on various fronts.
Both candidates promised similar free-market reforms while Juppé accused Fillon of plying a populist anti-Muslim, anti-immigration message.
They both pledged to cut public spending, reduce the number of civil servants, raise the retirement age from 62 to 65, end the 35-hour work week and cut business taxes.
Juppé tried to encourage conservatives to support a more tolerant approach toward France's ethnic, religious and social diversity.
Current polls suggest Fillon will stand a good chance of winning the Presidency in the April-May election - but will face a tough challenge in the form of far-right candidate Marine Le Pen, the leader of the Front National (FN).
In the first round of primary voting on Nov. 20, Fillon won 44.1 percent of the votes, Juppe 28.6 percent and Sarkozy 20.7. A second round was needed because no candidate secured a majority.
All French citizens over 18 — whether they are members of the Republicans party or not — were eligible to vote in the primary, if they paid 2 euros in fees and signed a pledge stating they "share the republican values of the right and the center."
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