John Longworth told the business group's annual conference on Thursday that the UK's long-term prospects could be "brighter" outside the EU.
The London mayor, a Leave campaigner, said Mr Longworth had been "crushed by the agents of Project Fear".
Number 10 rejected any suggestion they put pressure on the BCC to suspend him.
British voters will be asked whether the UK should remain a member of the EU in a referendum on Thursday 23 June.
The BCC, which represents thousands of large, medium and small businesses, has said it will not campaign for either side in the referendum as its membership is split.
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Although he stressed that he was expressing his personal opinion, in his speech Mr Longworth said the very best place for the UK to be was in a reformed EU, but "I have come to the conclusion that the EU is incapable of meaningful reform, at least in the foreseeable future".
Members were later told Mr Longworth had been temporarily suspended for breaching the group's official position of neutrality, the paper added.
Many of those working to leave the European Union present themselves as campaigners at odds with an overbearing establishment.
They will now ask whether anyone at Downing Street had any contact with the BCC before Mr Longworth's suspension, a question Number 10 sources has not yet been able to answer.
Any proof that Mr Longworth had been silenced by powerful enemies would strengthen that narrative.
For now, no proof has been presented, and Mr Longworth - who has not commented - finds himself at the centre of an increasingly ill-tempered row.
Mr Johnson said it was "absolutely scandalous that John Longworth has been forced to step aside".
"This is a man who reached the conclusion - after long reflection and a lifetime's experience of business - that it would be better to Vote Leave.
"He speaks for the many small and medium sized businesses - the lifeblood of the economy - who cannot understand why they should comply with more and more regulation, over which this country has no democratic control."
He added that it was not right that "when someone has the guts to dissent from the establishment line, he or she is immediately crushed by the agents of project fear".
The term "project fear" has been used by Leave supporters who accuse those backing Remain of "scaremongering" about possible repercussions of the UK leaving the EU.
has also reported that a friend of Mr Longworth claimed Downing Street had "bullied" and were "putting pressure" on BCC board members to suspend their director-general.
But a Downing Street source told the BBC Number 10 were as surprised by the news that Mr Longworth had been suspended as anyone, and strenuously denied any involvement in the BCC's decision.
"This is simply not true. This is a matter for the BCC. No pressure was put on the BCC to suspend John Longworth," they said.
A source for the campaign group Stronger In said allegations from pro-Leave campaigners that it was using scare tactics were a smokescreen to avoid answering difficult questions.
