Darragh Lenihan's own goal early in the second period restored the home side's two-goal advantage, which goalkeeper Ben Foster preserved with a penalty save to deny Adam Armstrong.
Mowbray was convinced however that the officials had blundered by showing Kabasele only a yellow card for tripping Armstrong to prevent him going clear when the game was less than 25 minutes old.
"An unbelievably poor decision from the referee could have been the thing that changed the game," he said.
"Armstrong was through. It was an unbelievable yellow as opposed to an obvious red. That's football and we have to live with it I suppose.
"We missed a penalty as well, which would have made the last 20 minutes interesting. The history books will say we got beat 3-1 but I do think it was a really poor decision not to show a red card.
"The referee said there was a covering defender. Well, I've watched it back and there is no covering defender that's getting anywhere near Armstrong.
"I'm quite excited by this team and think we are going to win a lot of matches. We are entitled to be disappointed – we let them off the hook."
The win moved Watford up to third but manager Vladimir Ivic made it clear there was no point getting too excited.
He said: "We can be satisfied with three points but we know that we have to improve a lot of things, like when we have possession.
"We have to learn to win because when you are relegated from the Premier League to the Championship you have a different goal.
"It is a good start from six games but the Championship is long. We are waiting for injured players to come back and help us."
Ivic was unclear whether Kabasele had been fortunate to stay on the pitch, as Mowbray had suggested, with fellow centre-back Ben Wilmot the man the officials judged to have been the last man.
"To be honest I don't know where Ben Wilmot was at that moment, whether he was closer to the keeper than Kabasele and the player of Blackburn," he said.