The midfielder was expected to make the trip but was not on the list of players confirmed for the team's flight to Portugal. The captain is currently recovering from a hamstring injury.
"He is just coming back from injury and is not ready to play in a game, but he is not injured," manager Arsene Wenger told the club's official website.
The 24-year-old was left out of the Emirates Cup last week after reportedly becoming unsettled by the constant rumours of his potential move to Barcelona.
Wenger added: "I do not want to speak about the transfer of Cesc Fabregas because I have done that three years now in every press conference so I do not think there is any more need to add something.
"I love Fabregas and want him to stay."
Arsenal, who rejected a bid of £27m from Barcelona on Friday, are reportedly holding out for £40m for the player.