The 11-billion dollar measure would cut Medicaid by $1.5 billion and also reduce mental health and addiction treatment programs.
Wednesday's vote was 0-67-45, with Democrats who control the House casting the "no" votes. The entire Republican caucus voted "present."
Democratic House Speaker Michael Madigan says the vote was intended to "facilitate consideration" of next year's budget.
Rauner has left the door open to new revenue sources but the Republican also wants lawmakers to approve his pro-business priorities.
House Human Services Appropriations Chairman Greg Harris says Rauner's proposal attempts to balance the budget "on the backs of the most vulnerable."