Moments after collecting a yellow card early in the second half following a challenge on Joe Allen, Alonso provoked loud appeals for a red from Stoke fans as he brought down Mame Diouf.
The calls went unheeded, with referee Mike Dean awarding a free-kick but keeping his cards in his pocket after lecturing Alonso, who was then substituted moments later.
And Hughes believes Antonio Conte’s decision to take Alonso off shows his Chelsea counterpart agreed that the left wing-back perhaps deserved a second yellow.
In his post-match press conference, Hughes said: “The referee has made a call on Alonso. He could have been sent off and should have been in my view.
“Their manager agreed he was lucky because he took him off. Those are the moments you need to go for you.
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“The referee allowed them to stop the game. Chelsea are very much a reflection of their manager in the way they manage the game.”
Chelsea were already two goals to the good by the time Alonso was taken off thanks to two first-half strikes from Alvaro Morata and Pedro.
Morata struck twice in five minutes late on for his first Chelsea hat-trick to add some gloss to a scoreline that reflected harshly on Stoke.