UEFA handed down the punishment, which includes a €30 million fine (£25m/$33m), to the Premier League giants for breaching Financial Fair Play rules.
Following an investigation, the Adjudicatory Chamber of UEFA's Club Financial Control Body (CFCB) found City guilty of "overstating its sponsorship revenue" between 2012 and 2016.
The investigation started after a series of allegations published by German magazine Der Spiegel in November 2018, which drew on documents purportedly obtained by whistleblowers Football Leaks.
UEFA's statement read: "The Adjudicatory Chamber, having considered all the evidence, has found that Manchester City Football Club committed serious breaches of the UEFA Club Licensing and Financial Fair Play Regulations by overstating its sponsorship revenue in its accounts and in the break-even information submitted to UEFA between 2012 and 2016.
"The Adjudicatory Chamber has also found that in breach of the regulations the Club failed to cooperate in the investigation of this case by the CFCB.
"The Adjudicatory Chamber has imposed disciplinary measures on Manchester City Football Club directing that it shall be excluded from participation in UEFA club competitions in the next two seasons (ie. the 2020/21 and 2021/22 seasons) and pay a fine of €30 million."
Denying any wrong doing, City responded with a statement on their website, saying UEFA made the decision even before the investigation had started.
"Manchester City is disappointed but not surprised by today’s announcement by the UEFA Adjudicatory Chamber," the statement said. "The Club has always anticipated the ultimate need to seek out an independent body and process to impartially consider the comprehensive body of irrefutable evidence in support of its position.
"In December 2018, the UEFA Chief Investigator publicly previewed the outcome and sanction he intended to be delivered to Manchester City, before any investigation had even begun. The subsequent flawed and consistently leaked UEFA process he oversaw has meant that there was little doubt in the result that he would deliver. The Club has formally complained to the UEFA Disciplinary body, a complaint which was validated by a CAS ruling.
"Simply put, this is a case initiated by UEFA, prosecuted by UEFA and judged by UEFA. With this prejudicial process now over, the Club will pursue an impartial judgment as quickly as possible and will therefore, in the first instance, commence proceedings with the Court of Arbitration for Sport at the earliest opportunity."