The defender was left out of the squad for the 1-1 draw with Everton at Goodison Park after Kean deemed he was not in the right frame of mind.
Samba submitted a transfer request after Rovers turned down two bids from QPR but the club have insisted he will not be sold in January.
Explaining his decision, Kean said: "It was a tough week. We've had a couple of bids for Chris from one club. We put out a strong statement, he handed in a transfer request so all those things put together, I thought it was best he wasn't involved.
"This is the last game for us before the window closes. He'll be back in next week and we can move on, get him back in for the next game and get him back playing."
The blow of Samba's absence was alleviated somewhat by the return from injury of Scott Dann, and Kean insisted there is no ulterior motive to their stance.
He added: "If Chris is going to move, it's not going to be in this window. It wasn't a case of trying to get teams bidding against each other to get a figure up, we'd just like to keep him, it's as simple as that.
"You could see we've got other lads we can put in, it was a tough decision leaving Grant Hanley out to put Scott Dann in so we've got real competition for places in the centre-half position and we want Chris to be one of those players competing and putting performances in for us, as he's done ever since he's been at the club."
Bolton's shock win over Liverpool meant a point was not enough to keep Blackburn out of the bottom three, and fans' protests against the club's owners Venky's will resume on the final day of the transfer window.
Supporters are unhappy that promised funds have not been invested in the playing squad, with striker Anthony Modeste, a loan signing from Bordeaux, the only recruit so far this month.
The 23-year-old made an appearance at Goodison Park as a late substitute, and Kean is confident he will prove to be a valuable addition.
The Rovers boss said: "We've been active, we've got Anthony in, initially until the end of the season. It was good to get him involved because he only trained with the lads for 20 minutes (on Friday) because we had to do his medical and do all his physical testing but he'll give us a different dimension.
"He's somebody that looks to run in behind, play on the shoulder of the centre-halves and now we've got all different types of strikers."
Another new face at Ewood Park this week was new assistant manager Eric Black, who has linked up with Kean following Paul Clement's departure for Paris St Germain.
Black was most recently Steve Bruce's right-hand man at Sunderland, and Kean said: "Myself and Eric go back a long time.
"He's an excellent coach, he's got a lot of Premier League experience as a coach working at a number of different clubs and I think his biggest attribute is the way he works on the pitch.
"Much like the staff we already have, he makes players better no matter what age they are."
Everton manager David Moyes was downbeat after the match and felt his senior players had failed to rise to the occasion as the Toffees made it four league games without a win.
He said: "I think we needed our better players to make things happen for us. Young Shane Duffy had a terrific game, he was arguably our best player and he's a young boy. We just needed a little bit more in every department."
