The duo were appointed in caretaker roles after Henning Berg's dismissal from Ewood Park after just 57 days in the job.
Berg's appointment came after previous manager Steve Kean parted company with Rovers following a sustained campaign for his removal from a section of the supporters.
Blackburn were third in the Championship when Kean left in September 2012 and they have since slipped to mid-table.
A statement on Blackburn's official website read: "Gary Bowyer and Terry McPhillips will remain in charge of first team affairs until the end of January.
"This decision follows discussions between the owners, directors and global advisor.
"The club would like to take this opportunity to thank Gary, Terry and the rest of the staff for their sterling efforts over recent days which have helped produce two successive and important league victories.
"The club's search for a new permanent manager will continue in earnest."
Bowyer ruled himself out of the running for the vacancy after guiding the team to a 3-0 victory over Nottingham Forest on New Year's Day
"I'm just giving the club a bit more time and then we'll see what that brings and what happens to myself and Terry," said Bowyer.
"We've been here a long time, myself and Terry, and we care about the club so we're just helping out as much as we can.
"We're just carrying on and we'll keep carrying on until we're told otherwise and that's all we know."