Many protesters gathered outside for the vote
The vote followed a passionate debate which was watched by a capacity crowd in the Edinburgh Parliament's public galleries.
The Protection of Wild Mammals Bill, sponsored by Labour backbencher Mike Watson, now goes forward for line by line scrutiny in committee.
MSPs were voting to agree to the general principles of the bill and they did so by 84 to 34 in its favour.
There was only one abstention over the move, and it is likely to be at least six months before the law comes into force.
Two wrecking amendments in the name of Labour MSP Elaine Murray and Holyrood's Rural Development Committee were both defeated.
The vote led to an unprecedented situation were the outcome flew in the face of a recommendation to reject the bill by the Rural Development committee.
Mr Watson called on MSPs to support the general principles of the bill.
It was first introduced in March last year and Mr Watson complained no other bill had taken longer than 107 days to complete its passage into legislation, while his bill was already on its 409th day.
He said its aim was to ban mounted fox hunting, stop hare coursing and ban fox-baiting where dogs were used to bait and fight foxes underground.
'Step forward'
Mr Watson said he was delighted: "I am obviously very gratified that the motion has been accepted by a reasonable majority to let the bill progress and to let other Members of the Parliament have an impact on how it will proceed from now on.
"We are now a step nearer to getting a ban on the sort of cruel activities I outlined in my speech.
"It would have been rather unfortunate, to put it mildly, if the Bill had been strangled at stage one. It would have been a big step back if the vote had been lost, but it's a qualified step forward."
Les Ward, chairman of the Scottish Campaign Against Hunting with Dogs, said it was a "historic" move as he predicted the result would be welcomed throughout the country.
He added: "This is a great day for Scotland's wildlife. For too long, a small number of individuals have been free to bait and bully wild animals for sport."
There was condemnation from pro-hunting groups, who vowed to continue their campaign to change the bill.
'Fight goes on'
The British Association for Shooting and Conservation said the Bill would threaten the future of working dogs in the countryside.
Director Colin Shedden said: "We will now have to spend a considerable amount of time and resources ensuring that the bill is radically modified and that its impact on those using gundogs, terriers and other working dogs is minimised."
Alex Hogg, chairman of the Scottish Gamekeepers Association, called on those who live and work in the countryside to unite against it.
He said: "We will fight on, we will not give up, for the work we do today is Scotland's tomorrow."