The mayor said there would be a new half-price travel scheme for people on income support, while the elderly and war veterans would still receive support.
He said his fares package would sustain funding for projects such as Crossrail and the transport improvements needed for the 2012 London Olympics.
Mr Johnson said the previous mayor's fares policy had been "unsustainable", removing more than £80m from TfL's funds this year alone.
"Some of us will pay a little more but I have ensured fares will remain affordable, especially for people who rely on public transport most, including the elderly, disabled veterans and those on lower incomes.
"I have been left to tackle the unfunded legacy of Livingstone's largesse.
"Put simply, the previous mayor's cynical and irresponsible pre-election fares freeze and support for unfunded transport schemes is unsustainable and has produced a gap that has to be plugged."
Mr Livingstone responded: "Londoners are beginning to learn the high cost of Boris Johnson.
"He promised to save Londoners money but instead, after just a few months in office, he is pushing up fares above inflation to pay for his own incredible waste of Londoners' money."
And Labour's London Assembly transport spokesperson, Val Shawcross, said: "Boris Johnson has given us no evidence whatsoever for his claim that there is a transport finance black hole.
"If the mayor genuinely is concerned about the fares budget then he should have thought twice about abolishing the £25 higher charge for gas guzzlers and should reconsider his expensive plans to replace the bendy bus."
London TravelWatch, the watchdog for London transport, said it regretted the rises but but accepts that these increases are required in today's economic climate.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.