The company has stalked the site at 452 St Kilda Road, which includes a heritage-listed mansion, since missing out on a bid to buy it from developer Clement Lee last year.
The unnamed buyer at the time is believed to have topped an offer by APBC, buying the heritage site for about $10 million. But the mystery buyer is believed to have struggled to move forward with plans for a residential tower.
A lawyer for APBC brokered the latest deal earlier this week.
APBC director Will Deague said the site appealed because it already had an approved permit to build an 18-level tower behind the heritage building, known as Yarra City House.
Mr Deague said APBC planned to build the approved design by MNG Architects, which includes 220 serviced apartments, 80 car parks and three cafes and bars. The project will cost about $90 million.
He said the heritage building would be restored to its former glory and used as a boutique commercial office.
Formerly called the Airlie, the residence was built in 1891 and was converted into a guesthouse in 1924. Until 1995 it was home to the Royal District Nursing Service headquarters.
Mr Deague said 452 St Kilda Road would be land banked for the time being as APBC pressed ahead with a bevy of boutique hotels and serviced apartments around South Yarra named after Australian artists. The developer recently acquired the former Hawthorn courthouse and police station at Glenferrie Road, which it plans to redevelop into 130 serviced apartments over five or six levels.
The company last month bought the Peninsula Centre in Frankston for $11.2 million, which it plans to turn into an $80 million, five-star hotel.