Victim Support Scotland chief executive Kate Wallace said the passage of the bill was a “momentous occasion”.
“It marks a significant step towards creating a system that considers and prioritises the needs of people impacted by crime,” she said.
There was broad agreement in parliament over abolishing the not proven verdict, but some opposition MSPs raised objections to pushing through such a wide range of reforms in one bill and being given limited time to debate complex amendments.
Tory MSP Sharon Dowry said the legislation would “waste millions on cosmetic solutions that will make little difference to victims”.
Labour justice spokeswoman Pauline McNeill raised concerns about taking serious sexual offence cases out of the high court and into a specialist court.
Her colleague Katy Clark added that the bill was “far too large” and that several amendments received too little scrutiny.
However, Scottish Greens justice spokeswoman Maggie Chapman said the bill would help deliver “compassion, dignity and justice for victims”.