Instead, Froome slipped quietly to the margins, relegated from Sky's undoubted leader to Thomas' domestique de luxe. As it transpired, the trusty lieutenant's restless desire to be the main man overwhelmed even his teammate's designs on joining the pantheon as a five-time Tour de France champion.
Froome, of course, can cite his share of mitigating circumstances. He was exhausted by his exploits at the Vuelta a Espana and the Giro d'Italia, which sealed his distinction as the first man to hold all three grand tour titles at the same time. He was emotionally bruised, too, by the inquest into his elevated salbutamol readings, the resolution to which came just five days before this summer's grand depart in the Vendee.
And yet one image on the Col du Portet, as the Sky convoy ascended inexorably into the mist, hinted at a more definitive power shift. Where Thomas looked unbreakable, never letting the steepening gradient disrupt his cadence, Froome's face was a mask of anguish as he saw his hopes of a fourth consecutive Le Tour triumph vanish.
They are close friends, living out of each other's pockets on Tenerife training camps and never displaying any animosity on the roads.
For any team, such solidarity is a precious asset, given how the Tour de France is littered with squabbling stablemates.
Since his challenge faded, Froome resigned himself to the futility of trying to rein in Thomas. Despite predictions that Thomas would wobble over the final hurdles, he has appeared stronger with each stage.
There is no disgrace for Froome in being beaten, but there must now be legitimate questions over his future. The panache with which Thomas rose to the top spoke not of an aberration but of a baton being handed over.
For a team as obsessed as Sky with creating a dynasty, there is seldom any room for sentiment.
Sir Bradley Wiggins was a national hero when he became the tour's maiden British winner in 2012, but at the first sign of weakness, Sir Dave Brailsford dropped him like a stone, not even selecting him for the team two years later.
Publicly, Brailsford has backed Froome, calling him a "titan" for offering support to Thomas en route to the finish line. But privately, Froome has to trust that his third place does not instantly bracket him as yesterday's man.
Tellingly, Froome acknowledged that Sky are looking elsewhere, describing how Egal Bernal, the team's young Colombian star, "has an amazing future ahead of him".
Having raced four grand tours in succession, Froome has earned the right to step away from the spotlight for a while, spending time with wife Michelle as they await the birth of their second child.
But on the evidence of the past three weeks, there is enough reason for uncertainty about where he goes next.
In 2014, he could blame the loss of his crown on broken bones in his wrist and hand. Now he has been outmanoeuvred by a cyclist previously considered a loyal deputy. In elite cycling, that is not a comfortable place to be.
A multiple Tour de France champion being usurped by an underling is rather like a breakaway rider being swallowed up the peloton. Beyond that point, the only way is usually backwards.
