Crouch headed home with his second touch after coming on as a second-half substitute at the Britannia Stadium, ending Hull's recent resurgence.
A lacklustre, scrappy first half ended without a single effort on target from either team.
Charlie Adam's introduction at the break gave Stoke a lift, but his two early efforts on Allan McGregor's goal both went wide.
Adam then turned provider for Crouch in the 72nd minute, as he lifted an inch-perfect cross into the penalty area for the veteran striker to nod home in trademark fashion.
Stoke - unchanged from last weekend's victory over Aston Villa - made a promising start, but were unable to turn possession in the final third into efforts on goal.
Victor Moses and Steven N'Zonzi both made good runs from midfield in the opening 15 minutes, only to be wasteful in the penalty area when under pressure.
Steve Bruce was forced into changes with Nikica Jelavic injured and Dame N'Doye dropped to the bench after returning home to Senegal, and Hull's play was affected early on.
It was not until the 20th minute that the visitors were able to pose a threat, as Sone Aluko skipped past Philipp Wolscheid but was unable to hit the target from a tight angle.
A scrappy end to the half saw Stephen Ireland lucky to stay out of the book for a tackle on David Meyler, but opportunities on goal were at a premium, with the hosts seeing a penalty appeal waved away when Aluko challenged Phil Bardsley.
Adam replaced Ireland at half time and he gave Stoke a spark in the early moments after the restart, the Scot driving narrowly wide with a long-range effort after 54 minutes.
The former Liverpool and Blackpool midfielder went agonisingly close to breaking the deadlock soon after, as he sent a 20-yard free kick just wide.
But with the game seemingly drifting towards a drab draw, a lovely move between Stoke's two substitutes finally opened the scoring.
Adam collected the ball 25 yards from goal and played an inviting cross towards the back post, where Crouch rose above Paul McShane to head past McGregor.
Hull boss Bruce introduced N'Doye and Abel Hernandez to try and rescue a point in the closing minutes, but the changes proved fruitless as Stoke held on to all three points.
