Middlesbrough lost 2-1 in Wales as two goals from Andre Ayew kept the hosts in the hunt for an automatic promotion place. The Ghanaian international scored in the 40th minute but Boro equalised through Sam Morsy in the first minute of injury time.
However, there was only frustration for the visitors by the full-time whistle as referee Gavin Ward awarded a penalty to Swansea following a challenge on Jake Bidwell from George Saville.
Ward had initially pointed for a corner before changing his mind and Ayew made no mistake from the spot, dispatching the spot-kick in the seventh minute of stoppage time.
Warnock was booked for his protests surrounding the decision while earlier in the game he felt more should have been done when Anfernee Dijksteel was forced off after a collision with Ryan Manning.
Warnock was also angered when Marc Bola's 25-yard strike found the back of the net soon after half time but the referee awarded a free-kick to the hosts following a coming together between Yannick Bolasie and Jay Fulton.
"I thought we were the best side on the pitch," he told Sky Sports.
"I didn't see them having many chances at all and we have been let down by poor officials really, nothing else."
He continued: "It is just the worst afternoon for many, many weeks - and we have had a few of those.
"You can't speak to them [the officials]. You can speak to them as they're coming off but you can't speak to them after a game now.
"The work our lads put in, the football that we played, we deserved better than that. We were let down by a team in black today, I am really disappointed."
On the decisive late penalty, Warnock added: "If you're not sure, you don't give it.
"They [referees] all want to get celebrity status, it is just wrong. My lads have been let down by a team of officials who weren't good enough today."
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