The Frenchman was part of a 25-man breakaway that managed to stay away from the chasing peloton, and while EF Education First-Drapac's Simon Clarke took a much-needed stage win for the American team – their first WorldTour victory this season, and only their fifth win of any kind this year – Molard took over the race lead from Team Sky's Michal Kwiatkowski.
"The original plan was never to get into the day's breakaway, but when I saw how the day's stage was unfolding, I thought, 'Why not go on the offensive and try to get in the breakaway?'" Molard said on his team's website.
He becomes the first Frenchman to lead a Grand Tour since Tony Gallopin held the yellow jersey for a day – Bastille Day – midway through the 2014 Tour de France.
It's also the first Grand Tour leader's jersey that Groupama-FDJ have held since Australian Brad McGee led the Vuelta for four days in 2005.
"It's amazing," Molard told Eurosport at the finish. "It's emotional having the leader's jersey at a Grand Tour. It's a big deal in my career, so I'll try to make the most of it. I started to think about it [the leader's jersey] only towards the very end of the stage. I was thinking more about trying to take the stage victory, which was never going to be easy.
"As there were 25 of us in the break, everyone was attacking near the end, and I was always marked. Eventually, I thought to myself, 'Let's just go for the GC and see what happens.'
"After I'd crossed the finish line, and saw that we didn't have that big of a gap over the peloton, I didn't think I'd done enough to take the lead," Molard admitted.
"There are now a couple of easier stages, so if I can hold on to the jersey until Sunday, I'll be very happy with that."
The Vuelta is Molard's second Grand Tour this year. He finished 38th overall at the Tour de France in July, despite having crashed heavily on stage 2, and went on to take 11th place at the Clasica San Sebastian in early August.
Earlier in the season, Molard took what was only the second victory of his pro career when he won stage 6 of Paris-Nice between Sisteron and Vence. The 28-year-old attacked with just over a kilometre to go, and crossed the line solo, just two seconds ahead of Lotto Soudal's Tim Wellens.
Prior to that, his first pro win had come on a stage of the 2015 Tour du Limousin while riding for Cofidis.
Molard made the move to Groupama-FDJ in 2017, and the team's clearly happy with Molard's progression, regardless of his efforts on Wednesday. On the same day that he took the Vuelta's red jersey, the team also announced that he'd been handed a two-year contract extension, which was apparently entirely unrelated.