Ospreys had led 17-9 at the break on Saturday thanks to tries from Aisea Natoga and Dan Lydiate - the latter crossing the whitewash on his first start for the club.
But three penalties after the break from replacement fly-half Steve Shingler moved the visitors back to within two points and made for a tense finish.
In the end it was Ospreys who held on to win 17-15 in the first of back-to-back games against their rivals to move back to the top of the table.
However, Rees insisted valuable points rather than their current league standing was more important after being pushed all the way by Scarlets.
"I'm relieved. We were poor second half, there is no doubt about that," Rees told Ospreys official website.
"Scarlets made everything as uncomfortable as they could and we did not react well to that.
"But it's points in the bag and in the intensity in the local derby, across the course of the season, you learn to take them, even though it feels like a slight hollow victory but it's still a victory nonetheless.
"Being top at the end of the year is pleasing but let's acknowledge the top five, there's going to be a lot of teams jockeying for position.
"You don't read too much into it. But it's points in the bank and gives us the stimulus for next week."
Rees' thoughts were echoed by Ospreys outside-half Dan Biggar - scorer of two conversions and a penalty - who was quick to acknowledge his side had been below par.
"It's an apology from us, we haven't played that badly for a while," Biggar told BBC Sport.
"We allowed the Scarlets to come at us, and we were lucky to get out of jail there.
"We played well in the first - in fact we played some good stuff - but we were off the pace after that."
Click here to see the best images from Ospreys' victory over Scarlets
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