The emergency vote follows the scandal surrounding Bill Walker, who was expelled from the SNP last year and whose criminal conviction for domestic violence prompted calls for a review.
Nationalists who voted against the pay proposals were Christine Grahame, Stewart Maxwell and Sandra White.
Ms Grahame, convener of Holyrood's Justice Committee, urged colleagues to defy the party whip and consider the matter further in light of Walker's resignation, warning against drafting proposals "on the hoof" and potentially censuring MSPs who are detained on remand and then found innocent.
Nationalists who abstained were Joan McAlpine, Adam Ingram and John Wilson, with Labour's Hugh Henry also refraining from the vote.
Other members to vote against the pay move were John Finnie and Jean Urquhart - both Independents - and Green Party MSPs Patrick Harvie and Alison Johnstone.
Walker was convicted of a string of domestic abuse offences against three ex-wives and a step-daughter 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.
The amendment to the Scottish Parliament salaries scheme was backed by 105 MSPs.