The two men disagree on public sector job cuts -- 500,000 for Fillon, 200,000-300,000 for Juppe -- and foreign policies
The contest between the two ex-premiers has taken a bitter turn, leading more than 200 Republicans lawmakers to publish a pro-Fillon column urging a more civilised discussion.
Whoever wins the primary is widely tipped to become next president after elections in April and May against a resurgent far-right National Front (FN) and weakened Socialist Party.
A poll published on Wednesday showed Fillon would win 65 percent of votes in the final primary vote on Sunday against 35 percent for the more centrist Juppe.
"I'm holding the line and am keeping a cool head, but by the look of things there's powerful momentum that has been unleashed," Fillon, a social conservative with bold economic reform plans, told Le Figaro newspaper.
Polls for the first round, however, failed to forecast Fillon as the overwhelming winner as he surged past Juppe and former president Nicolas Sarkozy, who was knocked out.
Juppe, a centrist 71-year-old who wants a "happy identity" for demoralised France, is banking on a strong showing in Thursday night's debate when he hopes to highlight his differences with Fillon.
The two men disagree on public sector job cuts -- 500,000 for Fillon, 200,000-300,000 for Juppe -- and foreign policies, where Fillon favours a softer line with Russia and an alliance with Syrian leader Bashar al-Assad.
Fillon, a devout Catholic, is also more socially conservative, opposing full adoption by gay couples. He also takes a harder line on Islam and the danger it poses to France.
Fillon wrote in his book "Beating Islamic Totalitarianism" that "the bloody invasion of Islamism in our daily lives could herald a third world war."
Juppe by contrast has campaigned as a unifier.
"There are two currents today: a divisive right and a right that brings us together," he told Le Parisien newspaper in an interview published Thursday.
But three days from voting, Juppe stands accused of aiming low blows against his rival in his bid to reverse the dynamic of the race.
On Tuesday, he questioned Fillon's views on abortion -- as a Catholic, Fillon says he is personally opposed, but will not change the law -- leading to an unexpected intrusion of religion into the campaign.
Despite France's staunchly secular laws and concerns about the place of Islam in the republic, the candidates have both competed to show their closeness to the teachings of Pope Francis.
"The influence of religion in the contest between Juppe and Fillon is worrying," said the leftwing Liberation newspaper on Thursday next to a front-page headline stating "Watch out, Jesus is coming back!"
A column published on Thursday in the conservative daily Le Figaro, signed by 215 Republicans lawmakers, including the head of their groups in the lower and upper houses of parliament, called for a "frank but respectful debate from both sides".
They also criticised Juppe's attacks on Fillon's economic programme, which Juppe has called "ultraliberal" -- an insult meaning "ultra-capitalist" in French politics -- and "brutal" in its scope.
After Donald Trump's stunning success in the United States, interest has surged in France's election where mainstream politicians are also seeking to stave off a challenge from a far-right candidate.
Marine Le Pen from the National Front is currently forecast to come first or second in the opening round of the election on April 23 with around 30 percent of the vote, but then fail in the run-off on May 7.
But the hardline French nationalist is hoping to gather momentum after Trump's success, pitching a similar anti-elite, anti-immigration and anti-globalisation message.
Le Pen says she wants to ditch the euro and organise a referendum on France's membership of European Union -- a move that would put the future of European integration at stake.