Toulouse had battled back from 19-6 down to level at 19-19 before Holmes knocked over consecutive penalties.
Mike Ford's Toulon raced into an early 21-0 lead as Mathieu Bastareaud, Xavier Chiocci and Liam Gill all crossed the whitewash with Pierre Bernard slotting over the conversions.
Stade's cause wasn't helped when Jonathan Danty was sin-binned for a dangerous tackle on Japanese fullback Ayumu Goromaru, but the visitors clawed their way back through tries from Jules Plisson and Alipate Ratini.
Bernard tacked on a penalty to make it 24-12 on 48 minutes and New Zealand World Cup winner Ma'a Nonu grabbed a fourth try for Toulon, again converted by Bernard, although the hosts missed out on a bonus point.
Earlier, Australian fly-half Zack Holmes kicked two late penalties to give La Rochelle a 25-19 win over Toulouse to move back into second place.
In a topsy-turvy match, Toulouse had battled back from 19-6 down to level at 19-19 before Holmes held his nerve to knock over his fifth and sixth penalties of the afternoon.
He finished with a personal haul of 20 points having also converted a 49th-minute try by winger Gabriel Lacroix.
On Saturday, rock-bottom Bayonne stunned leaders Clermont 22-14, registering their first win in almost three months despite playing with 14 men for the entire second half.
Clermont were missing five first-choice players away on French international duty and Bayonne, on an 11-match streak without a win, seized their chance to record a first Top 14 victory since they downed Toulon 28-23 on August 21.
Skipper and flanker Jean Monribot scored their only try in the 25th minute while Damian Penaud and Benson Stanley crossed for the league leaders.
Bayonne were reduced to 14 men after 36 minutes when Welsh prop Ben Borster was red-carded for a dangerous tackle.
Despite the loss Clermont stay top with Montpellier back in fourth place after a 25-20 win over Lyon.
All Blacks Tommy Taylor and Conrad Smith marshalled Pau to a convincing 26-17 victory over Racing 92 to snap a four-match Top 14 losing streak.
Taylor, capped three times by New Zealand and preferred at fly-half to compatriot Colin Slade, kicked four penalties and converted Pau's two tries from Watisoni Votu and Baptiste Pourailly to guide his team to a much-needed win.
Racing managed a sole James Hart penalty in the first half, before notching up two converted tries through Dimitri Szarzewski and Chris Masoe, also a former All Black.
"It's an important victory against opponents who wanted to play," said Pau coach Simon Mannix.
"It's a step in the right direction."
Racing, missing a raft of big names including Dan Carter, were left ruing their ill-discipline, lock Ali Williams having been yellow-carded early in the game for repeated fouls.