The 23-year-old set up James McClean moments before the first-half break to reduce their deficit after goals from Daniel James and Mike van der Hoorn had put them on the back foot.
Having seen Bruno Martins Indi and Thomas Edwards sent off, the Welsh tactician substituted the Nigeria international who had already received a caution.
And the gaffer has explained that the reason for pulling out his star midfielder was to avoid him been sent off which could have further affected them against Rotherham United on Saturday.
“He got frustrated because we were out of possession for a long time,” Jones told club website.
“I pulled him out because I did not want him to have a second booking because we already missing a couple tonight and to go to Saturday on a back foot is difficult.”
Etebo has been a consistent performer in his debut campaign with Stoke making 29 appearances, capping it with two goals.
The Potters, 15th in the log with 51 points from 41 games, will hope to bounce back to winning ways when they host Rotherham.