The vote took place last night despite calls from some MSPs to delay it for further deliberation, following the resignation of disgraced politician Bill Walker, whose series of criminal convictions sparked calls for a review.
SNP MSP Christine Grahame, convener of Holyrood's Justice Committee, urged her colleagues to defy the party whip and consider the matter further in light of Walker's resignation.
She warned against drafting proposals "on the hoof" and potentially censuring MSPs who are detained on remand but who are then later exonerated.
Walker was convicted of a string of domestic abuse offences against his ex-wives in a summary trial at Edinburgh Sheriff Court which only has power to imprison him for up to a year when he is sentenced on September 20, giving him the option of continuing as an MSP.
Walker initially rejected a motion to quit, signed by the vast majority of MSPs, and only relented on Saturday after proposals to dock imprisoned MSPs' pay were presented by the Scottish Parliament corporate body (SPCB).
The amendment to the Scottish Parliament salaries scheme was backed by 105 MSPs, with seven voting against and four abstaining.