US attempt to overturn Jones red card in Copa
US Soccer announced the protest against Jones' red, and a yellow card against striker Bobby Wood which also leaves him suspended for the semi-final, in a posting on Twitter.
Jones was given his marching orders early in the second half of Thursday's 2-1 quarter-final victory over Ecuador following a confrontation with Manchester United's Antonio Valencia.
The 34-year-old was issued with a straight red card after raising his hands towards Valencia's face during the skirmish although replays suggested he barely made any contact with the Ecuadoran wide player.
US coach Jurgen Klinsmann later described Colombian referee Wilmar Roldan's decision as a "disgrace."
"Unfortunately we lost Jermaine for that incident which is an absolute joke," Klinsmann said in a press conference.
"Because I was right there -- the fourth official made the decision, not the referee, he didn't see it. He followed the decision of the fourth official. It's a disgrace, a decision like that."
The United States face either Argentina or Venezuela in Tuesday's semi-final in Houston.