The party, which has been represented on the London Assembly since 2000, says it has now overtaken the Liberal Democrats in the capital.
In the Mayoral election Green candidate Jenny Jones received 98,913 votes compared to 91,774 for Brian Paddick, beating the LibDem candidate into fourth place.
In the London Assembly list vote the Greens received 189,215 votes compared to the Liberal Democrats who got 150,447.
The Greens held both the Assembly seats they were defending despite opinion polls suggesting they would lose at least one.
The LibDems dropped one seat to finish the race with two, their lowest ever representation at City Hall.
The Greens also came third in the Barnet and Camden, City and East, Greenwich and Lewisham, North East and South West constituencies.
Speaking on Saturday Jones said: “This is a wonderful day for Green politics.
“The almost exclusive focus on the two frontrunners in the Mayoral election meant that any other result was very unlikely, but our resolutely positive campaign has stuck to the issues affecting Londoners and the policies to address them. I am over the moon that these messages have resonated.”
Jones suggested the result had “dispelled the myth that when times are tough, green politics are a luxury.
“More and more Londoners are realising that social and environmental justice are tied together inseparably, and with more Assembly members the Greens can help ensure that the Mayor is held to account on his promises and that City Hall can help create a city more equal, affordable, healthy, and safe for everyone.”
She added: “This campaign has attracted some wonderful bright, dedicated and loving young people to the party, who will pick up the torch and carry it forward in the interests of London’s future.”
