The New Zealand club had been nominated as the Oceania Football Confederation's (OFC) representative, which is scheduled to begin on 2 February (AEDT).
However, the quarantine measures in place in New Zealand in relation to the coronavirus pandemic have led Auckland to pull out.
It had been set to face Al-Duhail in the opening game but that contest will now not take place.
A FIFA statement read: "FIFA has today [Saturday AEDT] been informed by Auckland City FC that, in light of the COVID-19 pandemic and related quarantine measures required by the New Zealand authorities, the club will be unable to participate in the FIFA Club World Cup 2020.
"Despite FIFA's regular exchanges with the club, New Zealand Football and the OFC in recent days, the requirements of the New Zealand authorities in relation to isolation and quarantine go beyond FIFA's remit and, therefore, it was not possible to reach a solution.
"FIFA together with the Qatari authorities, will implement a comprehensive medical and security protocol providing the safeguards required to protect the health and safety of everyone involved in the competition.
"Following the withdrawal of Auckland City, the FIFA Club World Cup 2020 will be contested by Al-Duhail SC, Al Ahly SC, FC Bayern Munich, Ulsan Hyundai FC, Tigres UANL and the winners of the CONMEBOL Libertadores final scheduled for 30 January [31 January AEDT].
"The first-round match will no longer take place and Al-Duhail SC will begin the competition in the second round. The competition format remains otherwise unchanged.
"The draw to finalise the pairings will take place in Zurich on 19 January [20 January AEDT]."