Bernal was running a close second to Alejandro Valverde at the Tour of Catalonia before crashing on the final stage.
"I've said it before, but it's the first time I've raced for three weeks, as a GC (general classification) leader so it's a bit of an unknown", said Thomas, after he and Froome trailed home over 18 minutes behind Spanish stage victor Omar Fraile in Mende.
"For Froome, it would be a record-equalling fifth Tour".
Slovak Sagan, however, went through the first three mountain stages with relative ease and had enough gas in the tank for the final effort in Valence, where he outsprinted Norway's Alexander Kristoff and Frenchman Arnaud Demare into second and third place respectively.
However, days before the Tour de France, the International Cycling Union cleared Froome to race.
Earlier Thomas and Froome were among the riders affected when farmers who rolled hay stacks across the course were sprayed by police.
Here, Press Association Sport breaks down the Team Sky leadership "battle" and looks at where it might be settled.
The stage taking the peloton from Carcassonne to the spa town of Bagneres-de-Luchon resumed after a 15-minute interruption. The defending champion is 11 seconds ahead of third placed Dutchman, Tom Dumoulin.
Dumoulin hoping for Thomas collapse
Thomas kept the overall lead for a fourth consecutive day before the race pauses for riders to rest on Monday.
Most of the bad behavior from a small minority of spectators has targeted Sky, who started the race under a cloud and are looking hard to beat. "Thankfully the effects didn't last long but temporarily everything was stinging".
Froome was more evasive when asked if he would attack Thomas if in a position to do so. Still, all riders wearing a Team Sky outfit are often being jeered from the roadside. It was the same descent where Italian rider Fabio Casartelli died in the 1995 Tour.
In 2018 Froome became the first Brit to win the Giro. "It was my first professional race and it was bad".
What this clearly reiterates is that, although he's had a run-in with authorities because of a doping product, Froome - who was exonerated for the Salbutamol case - is the best GC rider of his generation.
Thomas and Froome have been team-mates since the latter joined Barloworld in 2008, with both then making the move to Sky when the team launched in 2010. "You only have to look at what he did on Alpe d'Huez, for a 21-year-old, that's unbelievable", Froome said on Sunday.
Sky have been largely unpopular in France since Briton Bradley Wiggins won the Tour in 2012 to start a period of domination during which they have won the race in five of the last six years. And that's when the statements began to change a little.
"The road should remain free, we are not going to lock the riders in a stadium or on a tennis court", he said. "Then you have a team in the front".
Trump plans to give billions in aid to farmers hurt by tariffs
But in response to American tariffs, Beijing imposed its own on soybeans, in addition to other American agricultural products. Trump has threatened to ratchet that up to more than $500 billion, a move that has left financial markets uneasy.