Chelsea took a one-goal lead into the interval at the Britannia Stadium courtesy of Jonathan Walters' own goal, and they cut loose in the second half.
Walters headed into his own net for a second time before a Frank Lampard penalty and an Eden Hazard thunderbolt condemned Stoke to their first home defeat of the season.
"I was really pleased with the first half," said Benitez. "We worked very hard against a Stoke team who pushed us, yet we remained strong in defence.
"Obviously the second half was much better. With us a goal ahead, Stoke were more open.
"We had more space and used our quality and the understanding between the players was much better. Everything went well for us."
The knives were out for Benitez following the midweek loss to Swansea in the first leg of the Capital One Cup semi-final, but he believes the win at Stoke underlines the work being done behind the scenes.
He said: "We have a really good staff at Chelsea who work very hard. The players are happy and the atmosphere is good.
"Obviously you can't control the results but in terms of the atmosphere at the club, it's fantastic.
"Hopefully we can win one or two more games and people will realise we're progressing well. If you analyse the stats you will see that we are scoring more goals and conceding less than in the past. Things are going well."