Bayonne kept their Top 14 survival hopes alive on Saturday with a 24-19 win over Biarritz in a fiercely contested Basque derby.
Clermont moved level with Toulouse at the summit of the standings with a convincing win at home to Stade FranÃ§ais.
The result also guarantees Clermont automatic qualification for the semi-finals.
Agen secured their spot in the top flight for another year with victory over Toulon while Racing Metro took a step towards the play-offs thanks to a bonus-point win over Brive.
Mamuka Gorgodze scored a hat-trick as Montpellier smashed Lyon, who are now almost sure to be relegated.
In the late game, Castres boosted their play-off hopes with a big win at home to Bordeaux-BÃ¨gles, who are now deep in the relegation quagmire.
Perpignan 25-10 Toulouse
Agen 22-13 Toulonnais
Clermont 25-9 Stade FranÃ§ais
Montpellier 43-12 Lyon
Racing MÃ©tro 40-19 Brive
Bayonne 24-19 Biarritz
Castres 44-20 Bordeaux-BÃ¨gles
ASM Clermont Auvergne 25-9 Stade FranÃ§ais Paris
Parc des Sports Marcel Michelin, Clermont Ferrand
Clermont confirmed their status as the team to beat in the Top 14 as they secured qualification for the semi-finals.
As was the case in last week's European quarter-final, Brock James was on song with the boot, landing 20 points including a drop goal.
For Stade FranÃ§ais, qualification for the play-off has now become complicated as they now trail Parisian rivals Racing by six points.
With a much-changed team, Clermont led 13-3 at the break, thanks to a try from hooker Benoit Cabello.
Dominant at scrum time, the Parisians took the game by the scruff of the neck in the second half as Julien Dupuy kicked them back into contention.
But the power of the hosts' bench proved too much for Stade FranÃ§ais as James kicked les Jaunards to victory in the final quarter.
The win was Clermont's 41st in succession at home.
"I am very happy with the spirit in our team," said Clermont coach Vern Cotter.
"The players don't want to disappoint the fans at Marcel-Michelin Stadium and these four points for victory are very important."
Stade's Australian coach Michael Cheika insisted his team can still make the end of season play-offs.
"I am not even thinking about not qualifying, there are still three matches to go, so we will see," he said.
Pens: James 5
For Stade FranÃ§ais:
Pens: Dupuy 3
Clermont:15 Jean-Marcel Buttin, 14 Brent Russell, 13 Seru Nakaitaci, 12 Gavin Williams, 11 Julien Malzieu, 10 Brock James, 9 Ludovic Radosavljevic, 8 Alexandre Audebert, 7 Julien Bardy, 6 Jason White, 5 Loic Jacquet, 4 Julien Pierre, 3 Daniel Kotze, 2 Benoit Cabello, 1 Vincent Debaty.
Replacements: 16 Ti'i Paulo, 17 Lionel Faure, 18 Elvis Vermeulen, 19 Julien Bonnaire, 20 Kevin Senio, 21 Aurelien Rougerie, 22 Lee Byrne, 23 David Zirakashvili.
Stade FranÃ§ais:15 Paul Williams, 14 Paul Sackey, 13 Morgan Turinui, 12 Martin Rodriguez , 11 Djibril Camara, 10 Felipe Contepomi, 9 Julien Dupuy, 8 Sergio Parisse, 7 David Lyons, 6 George Smith, 5 Pascal Pape, 4 Anton van Zyl, 3 Rabah Slimani, 2 Laurent Sempere, 1 Olivier Milloud.
Replacements: 16 Aled de Malmanche, 17 Rodrigo Roncero, 18 Tom Palmer, 19 Pierre Rabadan, 20 Antoine Burban, 21 Jerome Fillol, 22 Julien Arias, 23 Stanley Wright.
SU Agen 22-13 RC Toulon
Stade Armandie, Agen
A bad week for Toulon got even worse as the home play-off that looked so sure a few weeks ago is now under threat.
Manager Bernard Laporte has been summoned before the FFR and is set to see his 60-day ban for criticising the local refs extended.
The result means that Agen are safe from relegation as they climb into eighth.
Toulon took the early lead thanks to Gaby Lovobalavu's try and were ahead 10-9 at the break.
But Brice Dulin's second-half try for the home side plus 17 points from the boot of Conrad Barnard saw Agen bring their losing streak to an end and deny Toulon a losing bonus point.
Pens: Barnard 5
Pens: Giteau 2
Yellow card: Giraud (Agen - 22nd min)
Agen: 15 Brice Dulin, 14 Saimoni Vaka, 13 Junior Pelesasa, 12 Jamie Robinson, 11 Silvere Tian, 10 Conrad Barnard, 9 Maxime Machenaud, 8 Marc Giraud, 7 Adri Badenhorst, 6 Jean Monribot, 5 Pat O'Connor, 4 Dewald Senekal, 3 Gert Muller, 2 Jalil Narjissi, 1 Semisi Telefoni.
Replacements: 16 Julien Janaudy, 17 Laurent Cabarry, 18 Thibault Lassalle, 19 Antoine Erbani, 20 Alexis Bales, 21 Manu Ahotaeiloa, 22 Miguel Avramovic, 23 Beka Sheklashvili.
Toulon: 15 Luke Rooney, 14 Alexis Palisson, 13 Mathieu Bastareaud, 12 Gaby Lovobalavu, 11 Benjamin Lapeyre, 10 Matt Giteau, 9 Matt Henjak, 8 Joe van Niekerk, 7 Steffon Armitage, 6 Pierrick Gunther, 5 Simon Shaw, 4 Bakkies Botha, 3 Davit Kubriashvili, 2 Mickael Ivaldi, 1 Romain Frou.
Replacements: 16 Jean Charles Orioli, 17 Eifion Roberts, 18 Jocelino Suta, 19 Juan Martin Fernandez Lobbe, 20 Joe El Abd, 21 Geoffroy Messina, 22 Fabien Cibray, 23 Carl Hayman.
Montpellier HR 43-12 Lyon Olympique
Stade Yves Du Manoir, Montpellier
A great result for Montpellier as a full house of points brings them to just one point behind third-placed Toulon.
It was on-way traffic as Georgian loose forward Gorgodze bagged a hat-trick. Montpellier led 22-0 at the break and added three more tries after the break.
Fabien Galthie's are looking more and more like a side that could repeat their surprise appearance in last season's final.
For Lyon, the ProD2 beckons.
Tries: Nagusa, Gorgodze 3, Creevy, Fernandez
Cons: Trinh-Duc 5
Tries: Bontinck, Grosso
Yellow cards: Sukanaveita (Lyon - 27th min); Fatafehi (Lyon - 68th min)
Montpellier:15 Lucas Gonzalez Amorosino, 14 Timoci Nagusa, 13 Geoffrey Doumayrou, 12 Santiago Fernandez, 11 Martin Bustos Moyano, 10 Francois Trinh-Duc, 9 Julien Tomas, 8 Alex Tulou, 7 Mamuka Gorgodze, 6 Fulgence Ouedraogo, 5 Thibault Privat, 4 Aliki Fakate, 3 Maximiliano Bustos, 2 Agustin Creevy, 1 Juan Figallo.
Replacements: 16 Erasmus Van Vuuren, 17 Na'ama Leleimalefaga, 18 Mickael De Marco, 19 Remy Martin, 20 Eric Escande, 21 Paul Bosch, 22 Thomas Combezou, 23 Giorgi Jgenti.
Lyon:15 Eric Tomamichel, 14 Franck Romanet, 13 Alipate Fatafehi, 12 Waisale Sukanaveita, 11 Remy Grosso, 10 Laurent Tranier, 9 Ricky Januarie, 8 Nicolas Bontinck, 7 Vincent Clement, 6 Eugene N'Zi, 5 Coenie