MSPs vote to back the general principles of the Referendums (Scotland) Bill, with 65 MSPs backing it and 55 against.
The Scottish government wants to hold a new ballot in 2020 and has tabled the Referendums Bill to pave the way.
There have been calls for parts of the bill to be amended, in particular over whether the Electoral Commission would test the question for "indyref2".
Constitution Secretary Mike Russell told MSPs he would discuss the issue of an indyref2 question with the Electoral Commission and introduce an amendment requiring a short bill to instigate the referendum.
Adam Tomkins, speaking for the Scottish Tories, insisted his party would oppose any attempt at another independence referendum every step of the way.
This was echoed by Labour MSP Alex Rowley who said "the bill is flawed, vote it down".
Scottish Green Party co-convener Patrick Harvie backed the bill but called for the indyref2 question to be tested.
The Lib Dems reiterated their opposition through Mike Rumbles, who called it "bad legislation".