Mauricio Pellegrino was left disappointed after a dominant second-half display went unrewarded for Saints at the bet365 Stadium.
Hosts Stoke City went in front through Mame Biram Diouf’s 40th minute header, before Fraser Forster saved Saido Berahino’s penalty to keep Saints within striking distance.
What followed after the break was relentless pressure from the visitors, who deservedly drew level through Maya Yoshida’s acrobatic volley, only to concede again as Stoke substitute Peter Crouch flicked in a cruel winner five minutes from time.
“We dominated them,” Pellegrino said. “We didn’t create much, but we always controlled the ball and never gave them the possibility to control the game.
“We conceded a couple of chances on the counter-attack, because Shaqiri is a clever player who was always looking for spaces behind our midfielders, but in the second half we were much better.
“We conceded from a corner and then we scored from a corner, but we also created a couple of chances in the first half that were clearer than the ones in the second half.
“We drew level in the game when we were much better than them, but then we concede the winning goal.
“We are disappointed because I think we played a really good game, putting them under pressure even from the beginning.”