The Frenchman collected the maillot jaune for the seventh time at the end of stage 11 in Toulouse, in which Tour debutant Caleb Ewan broke his duck as he sprinted to victory ahead of Dylan Groenewegen by the width of a wheel rim.
Now the Pyrenees loom as riders look to Thursday's 209.5km stage 12 to Bagneres-de-Bigorre, which takes them over the Peyresourde and the Hourquette d'Ancizan - two category one climbs to soften up the peloton before Friday's time trial and Saturday's summit finish on the Tourmalet.
Alaphilippe has a 72-second advantage over second-placed Thomas, but this is the terrain where he is expected to finally relinquish control.
The Deceuninck-Quick Step rider, King of the Mountains last year, has been determined to make the most of his position but has not targeted the general classification this year and will be nearing the limit of his resources.
"Every day is a new adventure in yellow, it's just so nice" he said.
"Whatever happens tomorrow, I'll be happy. I will try to keep it tomorrow, but Paris is a really long way."
And if not himself, Alaphilippe pointed to the defending champion when asked who might stand on the top step of the podium in Paris.
"Geraint Thomas looks really strong and confident," he said. "For the rest, I don't know."
For Thomas, Wednesday's 167km stage from Albi was a relatively stress-free one, certainly compared to the chaos of Monday's finale when crosswinds split the pack and several contenders lost 100 seconds.
A four-man breakaway featuring serial escapee Stephane Rossetto of Cofidis went up the road early on but were never given much of a leash with the sprint teams eyeing their final opportunity until next Tuesday's stage in Nimes.
Dangers were lurking, however, and Movistar's Nairo Quintana and Trek-Segafredo's Richie Porte had to race back on to the peloton after being caught by a crash 30km out.
Porte's team-mate Giulio Ciccone - who wore the yellow jersey for two days after finishing second on stage six to La Planche des Belles Filles - was not so lucky as he limped home with injuries that saw him lose his 10th place in the general classification.
Ewan suffered a blow when his lead-out man Jasper De Buyst landed in a ditch around 10km from the finish, and it was Groenewegen's Jumbo-Visma team who were best placed as they barrelled down the Boulevard Lascrosses - scene of Mark Cavendish's second career Tour stage win back in 2008.
Mike Teunissen, winner of stage one in Brussels, led out Groenewegen, but after he launched his attack 200 metres from the line, Ewan had the power to come around him and complete the set with victories now in all three Grand Tours.
"I can't believe it," Ewan said. "I've been close in the last four sprints and my team never lost faith in me and I never lost faith in my sprinting. I knew if everything came together I could be fastest on the day and today I showed that...
"Since childhood there is no other race I've dreamt of winning. Watching in Australia, the Tour seems so far away - I can't believe I'm even here, but to win a stage is a dream come true."
Alaphilippe's Deceuninck-Quick Step team-mate Elia Viviani was third and Bora-Hansgrohe's Peter Sagan fourth in the points leader's green jersey.
More remarkable was seeing Egan Bernal, not usually a man for the sprints, roll over the line in 13th place in the young rider's white jersey to remain four seconds behind Ineos team-mate Thomas.
Bernal and Thomas will now eye the mountains to come, though the Colombian does not expect major moves on Thursday.
"I think we should wait," the 22-year-old said. "We are in a really good position with 'G' second and for sure he can do a really good time trial, so we should not take any risks tomorrow."