His mood darkened further a minute from time when a mistake by defender Jose Miguel Fonte handed City striker Nicky Maynard the gift of a winning goal.
The Palace manager was on the pitch at the whistle encouraging a jubilant home crowd to applaud referee Rob Shoebridge which they duly did.
Warnock must now wait to see whether he features in Shoebridge's report.
The referee had a brought rudderless game into focus when disallowed a shot from West Ham loanee Freddie Sears with just over half an hour gone.
It followed a raid which took both City and the match officials by surprise.
Palace keeper Julian Speroni kicked long, Alan Lee flicked on and Sears wrong-footed Cole Skuse in the Bristol defence as he burst through with a rising shot.
As he whirled away to celebrate the ball was back in play and being scrambled away by City.
Palace players protested it had clearly gone over the line and the referee sought his assistant's advice, who shook his head an play restarted with a goal-kick.
Any angry exchange between Warnock with the fourth official went on for several more minutes and at half-time the teams were led off separately to avoid a further flashpoint.
Things began to look up for Warnock early in the second half when a tight offside decision went Palace's way after Paul Hartley's follow up shot had beaten Speroni.
Both sides sensed this was the game to be won after both had drawn their opening games but they shared a common failing in the final third.
Newly arrived from Celtic, Hartley, was the speedy midfield raider who stoked up most of Bristol's attacks.
They had gone into the game without two key defenders in Louis Carey and Liam Fontaine, who had both reported unfit in the morning.
That might have opened the way for Palace but their two frontmen of transfer seeking Lee and and the rangy Alassane N'Diaye threatened only occasionally.
The game was run by the two number eights, Hartley and Neil Danns.
Early on Danns broke through the home middle line and was close to claiming the lead then late on he so nearly seized the initiative for Palace when he want down under a challenge from Hartley 35 yards out and to the left of goal.
Matt Lawrence struck the kick well and only the fingertips of Dean Gerken in goal prevented it going in at the far post.