Toulon were soundly beaten at Montpellier last weekend, but responded by edging out Stade after the boot of Morne Steyn looked to have settled it at Stade Jean-Bouin.
Josua Tuisova scored the only try of the first half and added a second to bring Toulon level at 12-12 midway through the second period following four penalties from Steyn.
A drop-goal from South African fly-half Steyn put Stade back in front 11 minutes from time, but new signing Isa – in his second spell at the club – went over two minutes from time to give Toulon a third win of the season.
Lyon are up to third after a four-try 31-12 home success against Castres.
Toby Arnold, Mickael Ivaldi and Alexis Palisson scored first-half tries to put Lyon in command and Baptiste Couilloud added another after the break in a commanding display from Lyon.
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