Bojan Krkic's first Stoke goal handed the visitors an early lead at White Hart Lane, with Jonathan Walters doubling their advantage before the interval.
Nacer Chadli reduced the deficit with an excellent finish late on, but Kyle Naughton's red card halted Tottenham's resurgence as a well-organised Stoke claimed a deserved three Premier League points.
"I thought we were very good," Hughes said. "We have shown we are a capable team, and overall I am very pleased with what we produced.
"We had a game plan, we committed to it, and we understood what was required.
"We made it difficult for them to create anything of any real note, certainly in the first half, and were always a threat with the talent and pace we have in forward areas.
"Our plan was to use the counter-attack. There were certain areas we felt we could exploit. We sensed if we started quickly could use pressure [on Tottenham] to our own ends."
Victory moved Stoke into the top half of the league table, but injuries to Marc Wilson and Phil Bardsley put a slight dampener on things for the visitors.
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