The supporters, furious at Rapid's recent poor run, built a small wall to block the front door during the early hours of Saturday morning.
They attached a photograph of general manager Werner Kuhn with the caption: "I'm not allowed in."
Two weeks ago, Rapid fans boycotted the first half of a match against Wiener Neustadt.
Rapid's problems continued at the Gerhard Hanappi stadium as the blew a 1-0 lead, leaving new coach Zoran Barisic waiting for his first win since replacing Peter Schoettel who was fired after a cup defeat to third tier Pasching 10 days ago.
Deni Alar had put the 32-times Austrian champions ahead in the 63rd minute but Brazilian Alan replied almost immediately, then converted a 70th minute penalty.
Dusan Svento completed the win in the last minute.
Second-placed Salzburg, sponsored by energy drinks giants Red Bull, cut the gap with faltering leaders Austria Vienna, who visit FC Admira on Sunday, to one point with five games to go.