Israel–Premier Tech veteran Clarke is one of several Australians competing at this year's edition, though he remains the only stage-winner after conquering the cobbles in dramatic fashion on Stage 5.
The 35-year-old needed a photo finish to confirm his victory over the top of Taco van der Hoorn (Intermarché–Wanty–Gobert Matériaux) and was overcome with emotion after notching his maiden individual stage win at La Grande Boucle.
Clarke had been dealing with the effects of his exertions in the days since, but expects to be on the offensive once the race continues in the mountains.
"I had a couple of pretty grim days there but today was good," Clarke told SBS Sport after Stage 9 on Monday (AEST).
"Finally, the first day I’m feeling semi-normal again. I definitely did some muscular damage that day (in Arenberg).
"It was pretty grim for a few days there but it’s coming around now so, a rest day tomorrow and I’ll be good to go again."
Another rider in need of rest is compatriot Ben O'Connor, the AG2R Citroen leader who tore his glute in a crash that's seen his general classification hopes come to an abrupt end.
The Australian has struggled in the subsequent stages, but received a boost after teammate Bob Jungels secured a gutsy win on Stage 9, his first at the French Grand Tour.
"It’s a day to forget for me but I am so, so happy for the team and for him," O'Connor said.
"He’s given up so much over the last couple of years, just to try and find out his problems, and it just shows that commitment and a little bit of therapy really helps. I’m so proud of him."
"I’m not really going anywhere in a hurry and my glute, really, is just getting worse," he added.
"Maybe you’ll be surprised to see me later in the week but, at the moment, I can only think about how happy I am for Bob.
"I’m rooming with him at the moment in this Tour de France so at least I get to celebrate something."
The 26-year-old later revealed the extent of his discomfort in the saddle - the shooting pain akin to a knife wound in the back and troublesome enough to prevent him from pedalling.
Fellow Australians Caleb Ewan and Michael Storer have avoided injuries for the most part but have also struggled in recent times.
One rider who hasn't, however, is Nick Schultz of Team Bike Exchange-Jayco.
Schultz has found form at his debut Tour, and produced a promising display in the 186.3-kilometre journey from Aigle to Châtel.
"I was actually looking to get in the breakaway today," Schultz explained.
"I tried a bit at the start there; sort of fired a bullet just before the successful breakaway went.
“I felt pretty good and Whitey (team director Matt White) just said to only keep pushing on if a result was possible. I kept believing a decent result would be possible with the way the race was being ridden.
"I thought they’d do that hard category one (climb) at tempo and, if I could sniff the finish out, maybe hang on and do a bit of a kick but it was just a bit too long there and I’m not at the level of those other guys.”
In truth, it's been a tough race for the Australian contingent currently in France, but there remains plenty of time for each rider to return healthy and focus on stage wins.
The Tour de France now enters a rest day, with racing resuming on Tuesday night (AEST) with a 148-kilometre stage from Morzine les Portes du Soleil to Megeve. Watch all the action live from 9:20pm (AEST) on the SBS SKODA Tour Tracker, or 9:30pm (AEST) on SBS and SBS On Demand.
