MSPs voted by 69 to 59 in favour of seeking permission for a referendum before the UK leaves the EU.
Ms Sturgeon says the move is needed to allow Scotland to decide what path to follow in the wake of the Brexit vote.
But the UK government has already said it will block a referendum until after the Brexit process has been completed.
Prime Minister Theresa May, who met Ms Sturgeon for talks in Glasgow on Monday, has repeatedly insisted that "now is not the time" for a referendum.
Her Scottish secretary, David Mundell, has said that the timescale could include "the Brexit process, the journey of leaving and people being able to understand what the UK's new relationship with the EU is, so they can make an informed choice if there was ever to be another referendum".
But Ms Sturgeon, the Scottish first minister, said her mandate for another vote was now "beyond question", and warned it would be "democratically indefensible and utterly unsustainable" to attempt to stand in the way.
She told a debate ahead of the Holyrood vote that she was not seeking confrontation with the UK government, and only wanted "sensible discussions".
Ms Sturgeon said: "My argument is simply this: when the nature of the change that is made inevitable by Brexit becomes clear, that change should not be imposed upon us, we should have the right to decide the nature of that change.
"The people of Scotland should have the right to choose between Brexit - possibly a very hard Brexit - or becoming an independent country, able to chart our own course and create a true partnership of equals across these islands."
She added: "I hope the UK government will respect the will of this parliament. If it does so, I will enter discussion in good faith and with a willingness to compromise.
"However, if it chooses not to do so I will return to the parliament following the Easter recess to set out the steps that the Scottish government will take to progress the will of parliament."
The two-day debate in the Scottish Parliament started last week but was suspended as news of the terror attack at Westminster emerged.
MSPs were asked to mandate the Scottish government to take forward discussions with the UK government on the details of a section 30 order, which is needed to make a referendum legally binding.
Ms Sturgeon's minority SNP government was backed by the pro-independence Scottish Greens in the vote, with the Conservatives, Labour and Lib Dems opposed.
The first minister is now expected to make the formal request for a section 30 later this week - after Mrs May formally starts the Brexit process on Wednesday by triggering Article 50.
Scottish voters rejected independence by 55% to 45% in a referendum in 2014, but Ms Sturgeon believes the UK voting to leave the EU is a material change in circumstances which means people should again be asked the question.
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