Racing set to host semi-final
There were also Top 14 wins for Lyon, Castres, La Rochelle, Pau, Clermont and Brive.
Log leaders Montpellier and Racing have now been confirmed as hosts of the two semi-finals.
Lyon salvaged a playoff berth with two late scores to edge out La Rochelle as the French Top 14's regular season ended in high drama Saturday.
When prop Lekso Kaulashvili crashed over for an 80th minute try he gave La Rochelle a bonus point and, a 31-7 victory over Stade Francais and it seemed, a place in the playoffs.
Lyon, who started the day in fifth, had just conceded a try to fall behind against leaders, Montpellier, meaning La Rochelle were in.
But, even though the matches kicked off at the same time when the final whistle blew in La Rochelle there were more than 10 minutes to play in Lyon.
Frederic Michalak, who had come on as a second-half replacement, kicked a penalty to put Lyon ahead.
In the last minute, winger Xavier Mignot ended a bout of desperate Lyon pressure by racing over for an insurance try. Michalak converted and Lyon won 32-24.
Montpellier still topped the standings and have a bye in the playoff.
"I am happy with the performance of my players," said coach Vern Cotter. "They showed a good attitude against a good team."
"We will now look at the preparation for the semifinal."
La Rochelle won and missed their objective. Stade were humiliated but survived in the Top 14.
"We were keen to regret nothing, at least in this match," said Romain Sazy, the La Rochelle second row who lamented "Two too many defeats at home, and points left on the road."
As for beaten Stade, coach Olivier Azam said: "We've got a lot of work to do next season."
Castres, the team place above La Rochelle, ensured their playoff place would not be threatened by thrashing Oyonnax, the team a place below Stade, 54-3.
Oyonnax finished 13th and will playoff against the loser of the match on Sunday between Perpignan or Montauban, the top two teams in Division 2, for a place in next season's Top 14.
European finalists Racing 92 crushed Agen 42-13 to ensure second and a bye to the semi-finals which gives them a weekend off after they meat Leinster in Bilbao on May 12 in the Champions Cup final.
Toulouse, who lost 36-26 at Clermont, and Toulon, beaten 38-26 at Pau, kept third and fourth.
In the first round of the playoffs, Toulon will host Lyon and Toulouse will be at home to Castres.
Toulon quickly fell 16-0 behind at Pau but in the 29th minute got what they wanted.
Fullback Hugo Bonneval cantered through for a seemingly certain try, stopped and lobbed a gentle pass to winger Vincent Clerc who touched down for his 101st Top 14 try, the outright record.
At 36, Clerc has played sparingly this season and had been tied with Laurent Arbo since scoring a 100th try in March.
When he announced in April that this would his last season, Clerc said he wanted "to free myself from this weight of 100 tries. It is symbolic."
Clermont's victory over ancient enemy Toulouse changed little, the reigning champions finished an embarrassing ninth. But the home crowd was able to bid farewell to Aurelien Rougerie, who played alongside Clerc in the three quarters in France's 2011 World Cup final team.
Like Clerc, and the 35-year-old Michalak, who also played more than 70 games for France, Rougerie has announced his retirement, unlike the other two, his team is not going to the playoffs
At 37, Rougerie, who had played his whole career for Clermont, ran out alone before kick off to wave and perhaps shed a tear, his tackle battered face showed little.
"'Et voilà, c’est fini'!" he said after the game. "To finish like that in the middle of the pitch surrounded by teammates old and new, by friends and, above all, by these marvellous fans were very emotional.
"I will still be at the club next season to work on the coaching staff. I prefer to warn the players that I fully intend to martyr them after the awful season they have just had."
Meanwhile, Perpignan beat Grenoble 38-13 on Sunday to secure automatic promotion to the French Top 14 after four years.
Perpignan, who won the most recent of their seven French titles in 2009, struck early when Jonathan Bousquet touched down in the fourth minute. They led 14-13 at halftime in Toulouse.
Perpignan who finished top of the Pro D2 standings pulled away from Grenoble, who came third, with 24 points between the 52nd and 72nd minutes.
Bousquet, who kicked a penalty as well as converting all five tries, finished with 18 points.
Grenoble, relegated from the top flight last season, have a second chance to gain promotion. They face Oyonnax, who finished 13th in the Top 14, in a playoff next Saturday.
Racing 42 Agen 13
Lyon 32 Montpellier 24
Castres 54 Oyonnax 3
La Rochelle 31 Stade Français 7
Pau 38 Toulon 26
Clermont 36 Toulouse 26
Brive 22 Bordeaux 20