The complaint to the South American Football Confederation means CONMEBOL's disciplinary committee will now deal with the incident.
Uruguay's FA (AUF) said in a statement on Friday: “The AUF's executive committee decided to open the defence of the player Edinson Cavani. It denounced to CONMEBOL's disciplinary body the actions of the player Gonzalo Jara.”
With Wednesday's match in Santiago balanced at 0-0 after an hour, Jara gave striker Cavani a friendly tap and when he did not respond the 29-year-old Mainz 05 defender poked his finger up the Uruguayan's backside.
Cavani reacted by pushing Jara away gently but the Chilean fell to the ground as if he had been punched.
The incident brought Cavani his second yellow card of the game and Chile went on to score the winner with eight minutes left.
AUF Executive Secretary Alejandro Balbi told Reuters their complaint would be backed by “photographic images and video footage that we all know about and give proof of (Jara's provocation).”
Balbi also said that on Monday they would present their case to have the red cards issued to Cavani and Jorge Fucile overturned.
They would also include the fact that the referee had put in his match report that coach Oscar Tabarez had insulted him, a charge the Uruguay coach denies.
Defender Fucile was shown the red card near the end of the match for what looked a clean challenge on Alexis Sanchez.
After Fucile's exit, the match was halted for several minutes as Uruguay's players surrounded the referee, and officials and players from both sides scuffled on the field.
Tabarez joined in the protest but later denied having insulted Brazilian referee Sandro Ricci.
Uruguayan Adrian Leiza, one of the five members of the CONMEBOL disciplinary committee, said he and another Chilean member would leave the decision about the complaint to the other three members.
Chile's semi-final against Peru is scheduled for Monday.
Uruguay fans and media were outraged about the incident, with former captain Diego Lugano threatening to take the matter up with Jara when the sides meet again in 2018 World Cup qualifiers.
“We're going to have to have a word with that lad 'Jarita' (little Jara) when our paths cross,” the centre back said via Twitter.
Jara's team mates came to his defence and accused Uruguay of sour grapes.
“The Uruguayans are shameless,” David Pizarro said at a news conference on Friday.
“It is difficult for them to accept their defeat. It's a shame that they don't analyse the way Chile played the other night.
“We had 80 percent of possession. Two styles went head to head, and in my view, once more, good football won out - skill over the physical game.”
Original source: Uruguay complain over Jara-Cavani incident