Cereal Killer on Brick Lane was damaged on Sunday night during a demonstration about the "gentrification of parts of east London".
Boris Johnson tweeted: "Small businesses like Cereal Killer are the lifeblood of London's... economy."
His office added he was "deeply concerned" about the "unacceptable" violent elements of the protest.
Cafe owner Alan Keery told the BBC's Victoria Derbyshire programme he thought it was "incredibly unfair to target a small business for a larger problem".
"They're talking about gentrification but they've tagged us as the poster boys for it, and we're not the real problem here," he added.
A local estate agent also had its windows smashed. One man arrested on suspicion of causing criminal damage has since been released with no further action.
A spokesman for the mayor of London said: "The mayor fully recognises the importance of Shoreditch's unique character and the role it plays in London's success.
"He continues to work hard to strike a balance between residential and commercial properties and strong day and night-time economies."
Labour's mayoral candidate, Sadiq Khan, said: "There is no excuse for mindless violence and intimidation."
When Mr Keery opened the cafe with his brother in December 2014, it attracted criticism for its prices, which go up to Â£3.20 for a bowl of cereal.
The organisers of the protest advertised it on Facebook with a post saying: "We don't want luxury flats that no-one can afford, we want genuinely affordable housing.
"We don't want pop-up gin bars or brioche buns - we want community.
"Soon this City will be an unrecognisable, bland, yuppie infested wasteland with no room for normal (and not so normal) people like us."
Police in Tower Hamlets are appealing for witnesses to the disorder.
Superintendent Pete Turner said: "Officers are currently reviewing the CCTV from both the cafe and the local authority. Any individual identified as being involved in the violence will be actively sought, arrested and brought to justice."
The mayor of London has praised a cafe in east London which was attacked by anti-gentrification protesters.