The bill will create a register of lobbyists and new regulations in a bid to increase transparency.
Government business manager Joe Fitzpatrick said the bill struck a good balance between and encouraging groups to engage with parliament.
Labour decided to back the bill despite calling it "watered down" and "not fit for purpose".
MSPs voted unanimously to support the bill after contesting a number of amendments.
Concerns had earlier been raised that the bill did not cover modern communications such as emails or phone calls, with some MSPs saying the plans did not go far enough.
Labour introduced an amendment seeking to change this, as well as another with an updated definition of lobbying, but both were rejected.
Green MSP Patrick Harvie said it was "absurd" that "semaphore will be included in the bill but email is not", while Labour's Patricia Ferguson called the situation "ludicrous".
Mr Fitzpatrick said he had listened to the public and it was clear that the bill should not catch individuals acting on their own behalf.
He said the bill would not cause any erosion of the openness of the parliament, saying the new arrangements were "proportionate and simple".
Labour's Neil Findlay, who originally introduced a member's bill about lobbying, said the latest legislation had been "watered down" to "a bowl of rather meagre gruel".
He said the bill was "woefully inadequate" and "not fit for purpose", but said Labour would support it to at least get lobbying onto the statute book.
The Conservatives also backed the bill, with MSP Cameron Buchanan saying it had reached the correct balance.
Standards committee Stewart Stevenson welcomed the bill, and paid tribute to the late Labour MSP Helen Eadie, who had pushed hard for an inquiry into lobbying in Scotland.
The Scottish Parliament has passed a bill seeking to regulate the practice of lobbying.