Hull, vastly improved since the arrival of manager Marco Silva in January, registered a deserved equaliser when Harry Maguire finished via a deflection in the 51st minute.
Peter Crouch's accurate low header restored Stoke's lead in the 66th minute before Shaqiri settled the result, cutting in from the right before unleashing an unstoppable, dipping shot into the top corner.
"It was a big three points. An important three points. We've come through a period that was arguably our most testing of the season in terms of fixtures," Stoke manager Mark Hughes told the BBC.
"For the most part this season, we've picked up points against the teams below us and that's what we've done today. As a consequence of winning today, I think we can probably express ourselves a bit more in the remaining games."
Stoke, in 11th, have 39 points from 33 games. Hull are two points above the relegation zone with 30 points.
A vastly improved Hull, though, should be confident of picking up points from their next four games against Watford, Southampton, Sunderland and Crystal Palace.
(Reporting by Tom Hayward; Editing by Ed Osmond and Ian Chadband)
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