"I think we have two leaders", Bernal said in the immediate aftermath of the stage, then quickly corrected himself and said he wasn't sure.
Still, that didn't stop one spectator from placing an aggressive hand on Froome's back in a gesture that the rider did not appreciate.
"Froomey felt good - the plan was for him to have a go and for me just to follow".
Nibali, the 2014 Tour champion, was fourth overall and one of the few riders who appeared capable of challenging Thomas and Froome - who sit 1-2 - for the title.
As if Wednesday's victory to put him into the yellow jersey wasn't heady enough, in gripping scenes at the top of Alpe d'Huez yesterday Thomas went one better, surging to the top of the most famous climb in cycling while wearing the yellow jersey.
Thomas's victory leaves Sky boss Sir Dave Brailsford with an intriguing tactical dilemma.
"Don't touch the riders, don't spit at us. Voice your opinions all you want but let us do the racing".
Peter Dejong AP Fans lean in as leader Geraint Thomas and two other racers turn a corner
As the pace eased again, Landa got rejoined the group and immediately moved to the front, but Thomas marked his move and stormed past on the final bend to claim his second consecutive stage win.
Thomas not only crossed the line first, but also took the general classification lead.
Defending champion Chris Froome's Team Sky controlled the pace and prevented attacks as headwinds blew in the ascent of the col de la Colombiere. "There were two police motorbikes, but no barriers at that point", the Italian said. During the 1975 Tour de France, a French fan reached out and punched Belgian five-time victor Eddy Merckx in his lower abdomen near the finish line of the 14th stage, with the blow and a broken cheekbone suffered in a spill three stages later dooming his chances. Over three minutes in arrears with a time trial still to come on Stage 20, and now down to four team mates after Tony Gallopin DNF'd stage 12, the rest of the Tour will be tough.
The 33-year-old won his first Tour stage in 2008 and his last in 2016.
Rigoberto Uran, last year's runner-up, withdrew before the stage began, having failed to recover from a crash on the cobblestones in Stage 9.
Thomas maintained that Froome was still "the man" who knows how to win three-week races.
While all this was happening, behind the peloton a number of big names were climbing off - including sprinters Andre Greipel, Fernando Gaviria and Dylan Groenewegen.
Massive tornado damage in central, south central Iowa
Pella Regional Health Center spokeswoman Billie Rhamy said seven people injured at the Vermeer plant were treated at the hospital. The National Weather Service relayed reports of "catastrophic damage", with overturned vehicles and tops of buildings "gone".