The Premier League leaders raced into a 2-0 lead in a pulsating first-leg encounter with goals from the irrepressible Kevin De Bruyne and Gabriel Jesus in the first 11 minutes.
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The Frenchman, who is to leave Ma U on a free in June, has been touted to the English champions in recent weeks.
The Toffees’ day got off a terrible start even before a ball was kicked at Anfield as Burnley’s 1-0 win over Wolves dumped Everton into the relegation zone.
The Brazilian also provided the assist for Manchester City’s other goal, a stunning strike by Rodri.
Liverpool stormed to the top of the table by tearing Manchester United to shreds in a 4-0 win at Anfield on Tuesday.
The Red Devils were thoroughly outclassed in the opening 45 minutes, with goals from Luis Diaz and Mo Salah before interval.
Manchester City manager Guardiola saw his side go down 3-2 at Wembley after making seven changes to the team.
Jurgen Klopp’s side are chasing an unprecedented clean-sweep of the four major trophies in a single season.
Scuffles broke out late in the match and in the tunnel as Atletico Madrid’s frustrations at their failure to prise open Manchester City’s defence boiled over.
After securing a slender 1-0 advantage in the first leg last week, the Citizens played out a goalless draw at the Wanda Metropolitano on Wednesday night, which was marred by unsavoury scenes towards the end of the game.
The 36-year-old Fernandinho has less than three months remaining on his current deal at the Etihad Stadium.
In an interview with Telemundo, Guardiola discussed his time as coach of Barcelona and the influence Messi had on him.
Manchester City were twice pegged back at the Etihad Stadium after goals from Kevin De Bruyne and Gabriel Jesus were cancelled out by Diogo Jota and Sadio Mane.
Hosts Manchester City go into the game on 73 points, one ahead of Liverpool, having played 30 games each.
Current Brazil boss Tite recently confirmed that he plans to walk away from the Selecao after the tournament in Qatar.
The Belgian playmaker fired home from a tight angle after Phil Foden came off the bench to stunning effect in a tense and tight first leg at the Etihad Stadium.
The Citizens have yet to get their hands on the trophy of Europe’s elite club competition, but they came close last season, only to lose 1-0 against Premier League rivals Chelsea in the final.
The Reds knew that victory would see them leapfrog Manchester City, who faced Burnley later in the day.
Burnley remain in the bottom three and could be seven points from safety if Everton beat West Ham tomorrow afternoon.
The Citizens are currently one point clear of second-placed Liverpool at the top of 6 table, while Burnley occupy 19th, four points behind 17th-placed Everton heading into this weekend’s fixtures.