Mikel Arteta converted in the second minute of injury time after Chris Samba had flattened Marouane Fellaini, but amazingly it was the third penalty referee Lee Mason had awarded after giving Rovers two previously - both of which they spectacularly missed.
“The decision at the end, I felt Chris Samba got good contact on the ball and it’s about 15 metres away from him when he comes down on top of Fellaini, that was also a tough one to take," Kean told reporters.
“We’re aggrieved, we feel that Samba’s got up head and shoulders above anybody and Fellaini’s backing into him. We work a screen where we put Steven N’Zonzi in front of their dominant header so that he can’t have a straight flick.”
It was Mauro Formica and Junior Hoilett who failed to convert from 12-yards for Blackburn, but Kean refused to criticise either, instead priasing the duo for stepping forward.
“I think what happened is the lad that feels confident," Kean added. "David Dunn is our usual taker, but Junior stepped and then the second one I think David Goodwillie had his hands on the ball but Formica got it.
"I’ve not got a problem with the lads that take it, at least they showed the bottle to take it. It’s a tough one to take today, but overall I thought our positive play was really good.”
Asked if he felt his team deserved the three points over the course of the game, Kean added: “If I was sitting here and we only had a point, we’d be bitterly disappointed.
"I thought we controlled the game from the start to the finish, I thought in the second half we were fantastic, the amount of chances we made, but it’s a ruthless business and you’ve got to stick your penalties away.
“I think you lift the team up by picking the bones out of the game and seeing how good we were. I think if we were poor in the game it’d be tough to pick them up, but it won’t be hard to pick them up because we were 60 times in Everton’s box with 21 shots on goal.
He added: “I think we controlled the whole game, be it for a couple of penalties, but you’ve got to give credit to the players stepping up to take it. But we’ve hit the post, we’ve the bar.
"I think with the exception of the result, the performance was excellent, I don’t think there’s been too many times in the last year or so where we’ve controlled a game like that, I think we pinned Everton all the way back.”