Boateng was caught in the head by Tuncay Sanli's overhead kick during Saturday's Premier League clash at the Britannia Stadium and after lengthy treatment, the Dutchman was taken from the field on a stretcher to a waiting ambulance.
With Dowie having already made all of his substitutions, the Tigers had to play the last 15 minutes - plus the resulting eight minutes' injury time - with 10 men.
But the real concern was for Boateng, although Dowie said it was too early to assess whether or not he had fractured his jaw.
"There was a lot of blood in his airway and we had to suction that out as he was struggling to breathe," he said.
"By the time he left he was a lot more comfortable. He will have to stay in hospital and I'll see him overnight.
"It is a bitter blow, particularly the time it happened when we were in the ascendancy.
"It was a fantastic challenge and that is the type of character he is - but there was no malice from Tuncay as I think he was shocked too.
"It is a hell of a whack. It is a nasty injury but hopefully he is fine and there is nothing wrong with his jaw because that would be a real blow.
"We've had some curveballs thrown at us already but we've got to get on with it."
Stoke boss Tony Pulis also absolved Tuncay of any blame.
"It was unfortunate. I don't think 'Tunny' knew the lad was behind him so you can't apportion any blame," he said.
"It was disappointing and you never want to see that."
Striker Ricardo Fuller scored for the second successive match when he capitalised on a sixth-minute error by Paul McShane to clip a shot past Boaz Myhill.
But when the injured Jamaica international did not reappear for the second half there was a significant swing as Hull gained enough control to have scored an equaliser.
However, they were hampered by a numerical disadvantage after Boateng's injury and the extra space was exploited by Liam Lawrence in the 90th minute when Matt Etherington picked out his team-mate on the right of the penalty area and he fired past Myhill and into the far corner of the net.
Dowie was critical of his players' defending for the opening goal but praised their attitude in their second-half performance.
"The first goal is a schoolboy, joke goal," added the Tigers boss.
"It is one you can't afford to give away as it gave them a massive foothold in the game.
"First half, football-wise, we didn't get going but second half we were much better and were growing as a force in the game when we went down to 10 men."
Stoke moved up to 10th place and Pulis said he could now finally relax knowing his side were safe for the second successive season.
"I think 42 points will keep us in the Premier League for another year," he added.
"Credit to Hull, they gave it everything they had and there was a 10-15 minute spell in the second half when they had a lot of the ball."