The Ineos Grenadiers rider positioned himself at the front of the peloton before the race start before waving his hands and indicating that the peloton was to stay put.
Froome was then seen heading what looked to be a firm and frank discussion – at a distance – with race director Javier Guillén.
The protest was due to a decision by race organisers not to implement the the-second rule on stage 10 which meant Primoz Roglic was able to snatch the race leader's jersey off Froome's teammate Richard Carapaz.
Stage 10 had been designated as a flat stage, but a climb at the finish line created time gaps, and UCI commissaires decided to not use the three-second rule which led to the Carapaz losing La Roja to Roglic.
The three-second rule was introduced to make flat sprint stages safer, with gaps of three-seconds at the finish line needed to implement time gaps between riders, so that GC riders wouldn’t also fight for the line alongside sprint trains.
“We change the jersey now, for yesterday?” Froome asked Guillén.
“Because it changed the race. If we start and Jumbo have the jersey, they need to control. If we start and we have the jersey, we need to control. So it changes the whole race.
“We can’t talk about this later, something needs to be decided now.”
Froome's teammate Geraint Thomas took to Twitter to applaud the rider's actions.
"Great to see the peloton sticking together at the Vuelta. Well, apart from the usual suspects," he tweeted.
"My point is, pro cycling is nothing without the riders. Yet all the big decisions are made by suits and we are the last to know. The main reason we have no say is because we don’t ever stick together as a peloton."