Cowley saw his men capitulate at the John Smith’s Stadium having led 2-1 early in the second half.
He said: “I thought it was a car-crash of a performance to be honest.
“We looked well short of it, physically and mentally. We got bullied by a strong Stoke team.
“Despite that, we managed to get 2-1 ahead – but we still managed to lose it. Sam Vokes led the line brilliantly for them, and we couldn’t cope with him.
“It’s been a tough Christmas for the players we’ve had available but we capitulated. That’s hard to take, particularly at home.”
Cowley also had his say on a tannoy announcement that took place in the second half. The message to spectators was regarding offensive behaviour following chants aimed at Stoke’s James McClean.
McClean, who has been vociferous about sectarian abuse he has received, applauded when the announcement was made.
Cowley said: “There’s no place for discrimination of any type whatsoever. I’m sure the club will investigate this and make sure the people involved in it are duly punished.”
Stoke bossed the first half but only had a slender 1-0 lead courtesy of the excellent Vokes, to show for their efforts.
Town were well below par in the first half but two goals in the space of three minutes just after the restart saw them go 2-1 up.
First, Steve Mounie (48) thumped home a header for the Terriers from a corner before Danny Batth scored an own goal.
Nick Powell (57) slid home an equaliser before the visitors went back in front as Tyrese Campbell produced a classy lob in the 66th minute. Campbell (70) then notched his second with a fine finish before substitute Lee Gregory added gloss with the fifth in the 90th minute.
Huddersfield Town: Grabara, Simpson (Hadergjonajat 74), Schindler, Stankovic, Jaden Brown, Hogg (Campbell, 71), Chalobah, Bacuna, O’Brien, Ahearne-Grant, Mounie. Unused substitutes: Coleman, Koroma, Edmonds-Green, Duhaney, Daly,
Stoke City: Butland, Smith, Batth, Lindsay, Martins Indi, Allen, Powell (Gregory, 85), Clucas, Campbell, Vokes, McClean. Ward. Unused substitutes: Ince, Davies, Cousins, Collins, Woods.
Referee: James Linington (Isle of Wight)