The agencies had faced a convoluted conflict of interest which could have jeopardised the deal going through.
Former Boots adviser Gavin Anderson is working with Kohlberg Kravis Roberts (KKR) and Boots investor Stefano Pessina, who had an initial £9.7bn approach rebuffed on Monday.
Finsbury continues to counsel the high-street chemist. It also remains retained by KKR, but will not work with the PE firm on this specific deal.
KKR's bid was leaked last Friday, prompting Finsbury to initially agree to work for both the PE giant and Boots.The agency argued that ‘Chinese walls' would allow it to continue to do so.
But insiders told PRWeek that, by Saturday, Finsbury had told the parties that advising both would be difficult due to the high-profile nature of the deal.
At this point, GA - also retained by Boots after its £7.8bn merger with Alliance Unichem last year - had already offered to step aside and advise KKR.
A deal between the agencies and stakeholders was eventually reached on Sunday, but not until after Finsbury had been criticised in some media circles.
GA chief executive Richard Constant has advised Pessina for some time, and his agency also works for KKR in Asia, Australia and Japan.
How GA managed to avoid a mention in media coverage remains a mystery, but the agency suggested it had informed journalists early on in proceedings that it could not advise both sides.
Finsbury partner James Murgatroyd heads the Boots account.
SEPARATELY... Boots has ended its three-month hunt for a consumer agency. Lexis PR will work across its health and beauty range from April after a massive AAR search that saw expressions of interest from 60 agencies.