Prop Botha (elbow) has not featured since the Heineken Cup match against Biarritz in January, while out-half Humphreys (hamstring) has not played since the end of last month.
Andrew Trimble also returns on the right wing after missing the last two games through injury, but flanker Stephen Ferris continues to be ruled out with a knee problem.
Rory Best takes over the captaincy from Johann Muller on his return to the team. The Ireland hooker appeared as a second half replacement against Glasgow Warriors last weekend and will start this time alongside Botha and Tom Court in an all-international front row.
In the back row, Willie Faloon gains a start at openside flanker in place of Chris Henry who drops to the replacements bench.
The backline has also been reshuffled as Ruan Pienaar, the late penalty hero in Glasgow, reverts to scrum half to allow Humphreys don the number 10 jersey.
Adam D'Arcy comes in at full-back as Simon Danielli moves to the left wing and youngster Craig Gilroy provides back-up on the bench. The other wing berth is occupied by Trimble, who replaces Conor Gaston.
Acknowledging the province's recent run of five straight league wins, skipper Best said: "I've watched Munster for a few years now and that''s the thing about them, they're never beaten until the last whistle.
"There's no point ignoring what is very good about other teams and there's no doubt Munster have that.
"It's something that we've been trying to instil through Brian McLaughlin, 'hold on a minute, the game isn't finished until the final whistle'.
"Whereas in the past with Ulster teams, with five minutes to go and seven points down, not only do we not win the game, but we don't even get a losing bonus point."
ULSTER (v Scarlets): Adam D'Arcy; Andrew Trimble, Nevin Spence, Paddy Wallace, Simon Danielli; Ian Humphreys, Ruan Pienaar; Tom Court, Rory Best (capt), BJ Botha, Johann Muller, Dan Tuohy, Robbie Diack, Willie Faloon, Pedrie Wannenburg.
Replacements: Andi Kyriacou, Paddy McAllister, Declan Fitzpatrick, Tim Barker, Chris Henry, Paul Marshall, Ian Whitten, Craig Gilroy.