Ministry of Sound had feared the residential tower would lead to complaints about noise that would see the club closed down.
Chief executive Lohan Presencer said: "We are incredibly pleased that committee members have applied proper scrutiny to all aspects of the application and its relation to planning policy.
"Members have arrived at the correct decision and now is the time for all concerned to come together to find a positive vision for the regeneration of the Elephant and Castle. Ministry of Sound wants to play a key part in this".
Presencer said the nightclub would write to developer Christopher Allen to invite him to talks about the future of Eileen House.
Embryonic alternative plans, which have been drawn up with architects Marks Barfield, will now be explored further, he added.
Southwark Council's cabinet member for regeneration councillor Fiona Colley said the Eileen House site was a "prime location in central London, and in the Elephant and Castle regeneration opportunity area. Any improvement to this area would be of great benefit to local people".
"We are very keen to see a development go ahead on this site and will be looking into the next steps forward", she added.