The center-right candidate has repeatedly denied all accusations and pressed on with his election campaign despite a dip in popularity. His party has been pressed to look for alternatives for his candidacy, with his former primaries rivals among those rumored to be up for replacing him.
Fillon has called the media storm a "political assassination." He is expected to face investigators on March 15, after which formal charges may be made.
The first round of the French presidential election is scheduled for April 23, with the run-off set for May 7.
"They think that I am alone. They want me to be alone. Are we alone here?" Fillon said at Sunday's rally on the Place du Trocadero square, with the crowd chanting a resonant "no."
"Despite the fact that the accusations against me are unfair, insulting and are used for specific ends, I should apologize to you. In particular for the fact that I have to defend my honor and the honor of my wife while I should be defending the country," he said.
Fillon admitted to making a mistake by employing his wife as his assistant but vowed to press on with his campaign despite the mounting obstacles.
"It is my fault that the project which I represent has encountered such obstacles. I made the first mistake when I asked my wife to work with me. The second one was how I went about telling you about it," he told the crowd.
Over 40,000 people were set to attend, with Fillon's website asking participants to avoid bringing banners in order to avoid any controversy. Participants only brought French flags with them which they waved vigorously during the rally.
Despite the show of support, Fillon's chances of victory have waned. Recent polls indicated that Fillon's former primaries rival Alain Juppe could beat both right-wing Marine Le Pen and independent Emmanuel Macron in the first round of elections. Meanwhile, Fillon's own voter support slipped from around 25 percent to less than 20 percent as the Penelopegate scandal unfolded.
Several members of Fillon's campaign have decided to step down amid the scandal. Representative for European and International Affairs within Fillon's team Bruno Le Maire announced the decision to leave campaign on Wednesday. Spokesman Thierry Solere and political adviser Dominique Bussereau followed suit on Friday. Fillon's campaign chief Patrick Stefanini has also fled the ship.
"I will continue to tell my fellow party members that they both do and don't have a say, as the final say belongs to you," Fillon said at the rally.
Sarkozy met with party heavyweight and Senate Speaker Gerard Larcher as well as party Secretary-General Bernard Accoyer on Friday before talking to Juppe on Saturday.
On Sunday, Provence-Alpes-Côte d'Azur Regional Council President Christian Estrosi, a party member, said that the party plans to shortly propose a solution to the dead-end situation.
"We will voice an initiative on Fillon in the coming hours," Estrosi said.
The proposal may be made by the early hours of Monday, he added without outlining any further details, but noted that it was backed by several other regional heads, including Hauts-de-France's Xavier Bertrand and Ile-de-France council head Valerie Pecresse.