The £16.4 million deal was given the green light as an emergency measure by the council’s acting chief executive Clive Heaphy, but it also commits the council to development funding that will be £13.5 million more than was originally estimated.
It has agreed to buy the National Express bus depot in Perry Barr for phase two of the athletes’ village and the legacy residential development, and develop a replacement site further along Wellhead Lane.
The depot site is close to Alexander Stadium.
The sale and development funding agreement has been capped at £15.5 million but the costs had previously been forecast to be £2 million.
The other £900,000 relates to stamp duty and professional services costs.
It was necessary to give emergency approval because the council could not wait for agreement at the next scheduled cabinet meeting on January 21.
The previous cabinet meeting was on December 17, but the legal agreement was not finalised until December 23.
The city council is blaming limited information and costs being rebased to align with development timescales for the increase and is to investigate why the estimate proved to be so inaccurate.
The emergency approval followed consultation with the leaders of the political groups.
The replacement site will require compulsory purchase orders being made on the Anduff Car Wash and the George Ellison land, which will take effect in March. Car parts retailer Leacy MG is also on the site but its lease with the city council only runs until February 21.
The 12-day Games is currently budgeted to cost around £780 million, with a quarter being funded by the city council.
Birmingham was only awarded the Games in December 2017 after South African city Durban was forced to withdraw as host. It shortened the preparation time available and put extra pressure on property deals and development timetables.