The probe means Suarez, twice previously banned for biting, may be hit with another lengthy suspension despite escaping punishment during the match.
FIFA said Suarez and the Uruguayan FA had until 5 p.m. Brasilia time (2100 UK time) on Wednesday to "provide their position and any documentary evidence they deem relevant".
FIFA is probing what it called an apparent breach of two articles of the organisation's disciplinary code. One covers infringements and the other offensive behaviour and fair play.
Suarez and Chiellini clashed in the Italian penalty area 10 minutes from the end of the match which sealed Uruguay's progression and Italy's elimination from the tournament.
Chiellini furiously pulled open his shirt to show the mark to the referee.
Reuters photographs show what appeared to be bite marks on his shoulder and pictures also showed Suarez sitting on the ground holding his teeth immediately after the incident.
The Italians were still complaining about it when Uruguay's Diego Godin scored with an 81st-minute header to secure the win.
"It was ridiculous not to send Suarez off," Chiellini told Rai TV. "It is clear, clear-cut and then there was the obvious dive afterwards because he knew very well that he did something that he shouldn't have done."
Suarez contested that version of events, however.
"Those are situations that happen on the pitch. We were both just there inside the area. He shoved me with his shoulder, and my eye got left like that also," he said in reference to Chiellini's mark.
Uruguay coach Oscar Tabarez said he did not see the incident, and complained that the forward was being persecuted.
"It seems there is this animosity toward him and he is being persecuted by past events," a visibly agitated Tabarez said when repeatedly being asked about the alleged bite. "There are people hiding behind the tree waiting for something to happen."
Liverpool's Suarez was banned for 10 games last year after biting Chelsea's Branislav Ivanovic in a Premier League match and in 2010 he was suspended for seven games for biting PSV Eindhoven's Otman Bakkal while playing for Ajax Amsterdam.
He missed Uruguay's World Cup semi-final against the Netherlands four years ago after being sent off for a handball on the line that denied Ghana what would have been a match-winning goal in the final minute of extra time.
FIFA's rules allow the use of video or "any other evidence" to retrospectively punish players.
FIFA's disciplinary code sets a maximum ban of 24 matches or two years, but the longest suspension FIFA has imposed for an offence in the World Cup was eight games for Italy's Mauro Tassotti for breaking Spain's Luis Enrique's nose in 1994 with an elbow.
Uruguay could potentially play four more games in the tournament and it would be a surprise if Suarez were to be given a ban of a shorter duration.
Opinion in Uruguay, a country of around three million people sandwiched between powerhouses Argentina and Brazil, was divided over Suarez's latest antics.
The 27-year-old is regarded as something of a hero at home, having grown up in a poor family in the northwestern city of Salto where he looked after parked cars to help support his siblings after his parents split up.
"We needed to win, so if you have to hit you hit, if you have to bite you bite," said Barbara Giordano, a 26-year-old law student in Montevideo.
Some Uruguayans, however, were furious.
"This kid can't control his biting and attacking issues," said Luis Lara, a 52-year-old shopkeeper. "That makes all of us Uruguayans look bad."
Suarez's indiscretion sent the world's social media into meltdown and within minutes of the match ending #Suarez was one of the top-trending hash tags on Twitter.
A tweet from former Liverpool striker Michael Owen was typical of a wave of reaction from former players and pundits: "Tell me I'm seeing things. Surely Suarez didn't bite someone again?," he wrote.
"I'm genuinely gutted. I love watching him play more than any other player but he obviously can't control himself."
Suarez, England's Footballer of the Year, scored both goals in Uruguay's 2-1 victory over England having missed the opening match as he recovered from knee surgery, and until the incident had kept control of his temper during a bruising game.
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