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While the Gunners were always determined to keep Fabregas, who joined them from the Spanish club in 2003 as a raw teenager, it became clear this summer the player was no longer committed to the Arsenal cause.
The European champions had seen a £27million offer rebuffed earlier in the summer as Arsenal remained steadfast in their demands over a £40million fee for their midfielder.
However, with Barcelona not willing to significantly up their cash bid, and Gunners manager Arsene Wenger admitting the player was unsettled, Arsenal reluctantly have allowed a cut-price deal to go through.
The package is widely reported to include a down payment of 30 million euros (£27million), with an additional 6m euros (£5.2m) in performance-based add-ons at a later stage.
There are also suggestions Fabregas is prepared to waive the £4million compensation he would be entitled to for the remainder of his long-term Arsenal contract, as technically the player never asked for a transfer.
In a statement on Arsenal's club's official website, Wenger expressed his disappointment at Fabregas' departure.
"We have been clear that we didn't want Cesc to leave and that remains the case," he said.
"However, we understand Cesc's desire to move to his home town club and have now accepted an offer from Barcelona.
"We thank Cesc for his contribution at Arsenal and wish him future success."
Fabregas had, officially at least, been struggling for match fitness because of a hamstring injury which saw him miss the club's Asia Tour and other pre-season games.
Wenger consciously omitted his captain from the Emirates Cup and the World Cup winner was not selected for Saturday's opening Barclays Premier League fixture at Newcastle, which ended goalless and saw summer signing Gervinho sent off.
Fabregas joined Arsenal for nothing from Barcelona in 2003, and has made more than 300 appearances, scoring 57 goals.
However, despite winning both the European Championships and World Cup with Spain, club success has not followed for the midfielder, who missed the Gunners' shock Carling Cup final defeat at Wembley through injury.
Fabregas is now set to agree personal terms and undergo a medical on Monday before sealing his return to the Nou Camp.
Wenger, meanwhile, will face the media ahead of Arsenal's crunch Champions League play-off against Udinese, which were Fabregas to have played would have made him ineligible for any other club later in the competition.
The Gunners boss will now be under more pressure to spend the proceeds of Fabregas sale - and indeed the Emirates Stadium coffers could yet be swelled further should contract rebel Samir Nasri also move on before the transfer window closes, with Manchester City said to be ready to bid £22million for the France midfielder.
Wenger, though, has already ruled out a swoop for Juan Mata from Valencia, but could yet look to push through a £15million deal for Shakhtar Donetsk's Brazilian midfielder Jadson.
Nasri will not be available for the first leg of the Udinese tie because of UEFA disciplinary sanctions, which also mean Wenger must serve a touch-line ban following the fall-out from their Champions League exit in Barcelona last season.
Striker Robin van Persie, likely to be the new permanent Arsenal captain, will also be suspended after his red card in the Nou Camp.
Midfielder Alex Song, meanwhile, could yet find himself on a charge from the Football Association for appearing to stamp on Newcastle midfielder Joey Barton, an incident which was missed by referee Peter Walton during Saturday's ill-tempered game at St James' Park.
Barcelona anticipate no late hitches and have announced details of how Fabregas will seal his return to the club.
They stated, on their official website, that Fabregas will have a medical test at Barcelona Hospital at 8am (7amBST) before undergoing a further test at Barcelona's medical centre at 10.30am (9.30amBST).
At 12.30pm (11.30amBST) he is due to sign his contract, which will be followed by photo opportunities and, at 2pm (1pmBST), a press conference with Fabregas.
Fabregas Factfile
1987: May 4 - Born in Arenys de Mar, Catalonia.
1997: Joins Barcelona youth set-up.
2003: August - Top goalscorer and wins adidas Golden Shoe for being best player at the FIFA Under-17 World Championship.
September - Signs for Arsenal.
October 28 - Becomes the youngest player in Arsenal's history when he plays against Rotherham in League Cup.
2005: May - Helps Arsenal win FA Cup.
2006: March 1 - Wins first cap for Spain, featuring against the Ivory Coast.
March 28 - Scores in first-leg win over Juventus in Champions League quarter-final.
May 17 - Plays as Arsenal are defeated by Barca in the Champions League final.
June 14 - Became youngest player in Spanish history to participate in a World Cup when he features against Ukraine.
October 19 - Agrees new eight-year deal with Arsenal.
2007: July 13 - Admits to having met with Real Madrid president Ramon Calderon and sporting director Predrag Mijatovic about a move to the Spanish club, but following Thierry Henry's move to Barcelona says he could not leave Arsenal "in the lurch".
2008: May - Voted the PFA's Young Player of the Year.
June 29 - Starts as Spain win Euro 2008 final 1-0 against Germany.
October 7 - Reveals it would be a "dream to return to Barcelona some day".
November 24 - Named Arsenal skipper after William Gallas is stripped of captaincy.
December 23 - Ruled out of action for four months after sustaining a knee injury.
2009: March 17 - Denies an allegation of spitting at Hull assistant manager Brian Horton after Arsenal's 2-1 FA Cup semi-final win, although he is later charged and then cleared.
2010: April 26 - Included in the PFA Team of of the Year.
May 20 - Named in Spain's 2010 World Cup squad.
June 1 - Barcelona submit a written offer for Fabregas and enter "formal" discussions.
June 2 - Arsenal release a statement saying they have rejected the offer and have no intention of selling.
June/July - Makes four substitute appearances in seven games in Spain's triumphant World Cup campaign, setting up winning goal for Andres Iniesta in the final.
August 6 - Vows to respect Gunners' decision not to sell him and insists he will be "100% focused on playing for Arsenal" this season.
2011: March 8 - Apologises to Gunners fans after making mistake in the build-up to Barca's first goal in a 3-1 Champions League win over Arsenal at the Nou Camp.
June 20 - Barca president Sandro Rosell admits Catalan club are unwilling to meet Arsenal's £35million valuation of Fabregas.
August 9 - Included in Arsenal's Champions League squad for play-off round tie with Udinese.
August 14 - A deal is agreed in principle between Arsenal and Barcelona for Fabregas to return to the Nou Camp.