Pulis announced he would miss tonight's match following the death of his mother earlier today, but with Stoke trailing 1-0 at half-time, Pulis came out for the second half to a huge response.
Etherington revealed Pulis had come in as he was so unhappy with what he had seen in the first half.
"Obviously he wasn't happy at half-time, he was very disappointed about what was happening," he told Sky Sports. "He had thought it would be too much to be with us but after the first half and the way we played he came in.
"They were on top and he wasn't happy, so he came in and I think we were better in the second half."
Kenwyne Jones headed home the first from Etherington's cross before Robert Huth scored with almost the final kick of the game - also from an Etherington ball.
"In the first half we were sitting back too much, but in the second half - after the manager had had his speech - we came out and went for the win," Jones said, who celebrated his first Britannia Stadium goal for Stoke with a back-flip.
"The back-flip has not happened for a long time, but tonight I'd had a couple of chances and it was a great ball from Matty and I finished it."
Villa caretaker manager Kevin MacDonald - continuing to stand in as Gerard Houllier works out his release from the France Football Federation - downplayed the effect of Pulis' arrival.
"We still had chances in the second half as well and I thought we played some good football in both halves, so its obviously disappointing that we lost 2-1," he said.
"We're always confident in the way we play, passing it, moving it around and creating chances but Stoke are always very difficult to beat as they showed in the second half."
Villa were left fuming with a free-kick decision in the build-up to Stoke's winner, as Jermaine Pennant appeared to go down easily under a challenge from Stylian Petrov, who was booked after the final whistle as his protests continued.
"They felt that Jermaine fell over rather easily for the free-kick, and we were very disappointed with a referee's decision that ended up conceding the winning goal," MacDonald added.