La Rochelle took over as Top 14 leaders with a 26-14 victory over Montpellier before Toulon extended Lyon's run of defeats to four on Saturday.
Montpellier were beaten by Racing 92 last weekend and La Rochelle replaced them at the summit after Alexis Bales scored 16 points with the boot at Stade Marcel-Deflandre.
A first-half try from Paul Jordaan and another late on from Brock James sealed the top-of-the table tussle, putting the home side two points clear at the top.
Romain Ruffenach scored the only try for Vern Cotter's men in the second half and they must regroup ahead of a European Champions Cup clash at Glasgow Warriors on Friday.
Third-placed Lyon's slump continued at Stade Mayol, where Chris Ashton scored a try in each half as Toulon eased to a 39-11 win.
Toulon had also lost three in a row before Lyon made the journey south, but an Ashton double following a Mathieu Bastareaud try put them in control.
Xavier Chiocci and JP Pietersen also touched down as Lyon could only muster a Liam Gill try right at the end and two Frederic Michalak penalties.
Brive came out on top in an entertaining battle of the bottom two, beating Oyonnax 33-30, while Pau got the better of Bordeaux-Bagles 27-17 and Castres scored six tries in a 41-31 win at Toulouse.