He joined Barcelona's technical staff to scout opponents before Vilanova appointed him as his assistant last summer.
Vilanova's temporary departure led to the battlefield promotion of assistant manager Jordi Roura.
Elsewhere, Barcelona welcomed coach Tito Vilanova back from cancer surgery with a comfortable 4-0 win over city rival Espanyol.
So by the middle of the second half it was clear that Vilanova was ready to throw in the towel.
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Both trained alongside coach Tito Vilanova, who ran just his second session since returning from cancer treatment in New York.
Since taking charge of Barca, Vilanova has won 23 of his 27 matches in all competitions, suffering just two defeats.
Barca president Sandro Rosell said last weekend he hoped Vilanova would be fit to return to work in two-to-three weeks.
Instead, the players have vowed to overcome Milan for their manager, Tito Vilanova, who is undergoing cancer treatment in New York.
"I would like to thank everyone for their support, " Vilanova told reporters.
Between 2008 and 2014 with Guardiola and Vilanova as coach and assistant, the Catalan club won 14 trophies, including two Champions League titles.
David Villa -- who also came on as a substitute -- rounded off a resounding win for Tito Vilanova's men with a injury-time strike.
Borja Gomez put through his own net in injury time from Lionel Messi's cross to add gloss to the scoreline for Tito Vilanova's men.
Vilanova, who is undergoing treatment for cancer, left deputy Jordi Roura in charge, but it made little difference as Barca continued its hot streak.
Vilanova missed Saturday's 2-2 draw with Celta Vigo, in which Messi became the first player to score against every team in the league in successive matches.
Alexis Sanchez scored twice after the break as the La Liga leaders set up a quarterfinal clash with Malaga, despite the absence of coach Tito Vilanova.
But when Javier Pastore shook the very foundations of one of Europe's greatest bastions, a cloud began to descend upon manager Tito Vilanova and his ailing players.
"We trained today but he wasn't comfortable, and we decided that if we were going to risk him it would be at the end, " Barcelona coach Tito Vilanova said.
As a youngster Vilanova was at Barcelona's youth academy -- La Masia -- with Guardiola, though unlike the former Barca captain he failed to graduate to the first team.
But if the current Spanish champions are to triumph, they will have to stop Messi and his accomplices, who continue to prosper despite the absence of coach Tito Vilanova.
Vilanova, who was present for last weekend's 4-0 win over city rival Espanyol, faces six weeks of chemotherapy and radiotherapy following the operation which took place on December 20.
The relationship between the two has remained cool since Rosell was elected, but on the pitch under former coach Pep Guardiola and his successor Tito Vilanova, the triumphs have continued.
Even with Roura on the sideline, the club has said that Vilanova remains intimately involved in day-to-day events, watching film, receiving updates after practices, and setting the team's overall philosophy.
Vilanova underwent an operation to remove a tumor from his lung after suffering a recurrence of a problem on his parotid gland -- located at the back of his mouth.
Barcelona manager Tito Vilanova said Messi wasn't injured, but felt at the end of his last game that he was on the verge of injury after recovering from a hamstring problem.
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The allegations come as Barcelona has suffered a mini slump in form, twice losing to rivals Real Madrid and having to cope with the absence of Vilanova, who is battling cancer.
"Our style of play is so different from the rest of the teams that it's just easier to send out a guy that grew up playing our style football, " said Vilanova.
By that stage Tito Vilanova's side, much-changed from the trip to Paris, were already five goals ahead as both Fabregas and Sanchez netted twice in the opening period, toying with the visiting defense.
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Vilanova went on to play for some of Spanish football's lesser known clubs -- Figueras, Celta, Badajoz, Mallorca, Lleida, Elche and Gramenet -- before retiring as a player in 2002 and turning to coaching.
Vilanova's team, under the temporary guidance of assistant Jordi Roura, is looking to continue a run which saw them pick up a record 16 wins from their first 17 league matches of the season.
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