Everton supporters group 1878s shared a video of the banner before the plane took flight. The banner was flown after the Merseyside club were handed a 10-point deduction last week for breaching Premier League's profitability and sustainability rules.
The penalty dropped them from 14th on the table and into the relegation zone in a ruling that rocked the league. City are facing 115 charges for breaking the league's financial rules.
The banner, which flew past the stadium in the second half, was the second displayed in the skies over Etihad during the game. Earlier, a plane flew with a banner organised by human rights group Amnesty International that read "UAE: Free Ahmed Mansoor."
The activist was jailed in 2018 for 10 years in the United Arab Emirates. City owner Sheikh Mansour is the UAE's vice-president and deputy prime minister.
"Freedom of expression is a human right," Amnesty International said in a statement. "Ahmed should not spend a day longer behind bars. Ask the UAE Ambassador to help secure his immediate release."
Everton supporters, meanwhile, plan more protests on Sunday when they host Manchester United at Goodison Park.
Everton manager Sean Dyche said on Friday that the club were shocked by the "disproportionate" punishment, while Guardiola argued that City were innocent until proven guilty and called Everton's case "completely different."
