Owen was introduced 16 minutes from time after Newcastle had surrendered the lead given to them by Nicky Butt's 42nd-minute strike when Andy Johnson struck eight minutes after his arrival as a half-time substitute.
The former Liverpool frontman played a pivotal role in his side's win, sending in the cross which was cleared to Emre to blast home a 25-yard shot four minutes from time.
Emre then returned the favour for Owen to score his third Newcastle goal this season and his sixth in total in the final minute, although the visitors pulled one back in injury time when goalkeeper Shay Given could only palm Mikel Arteta's deflected cross into his own net.
"But at the end of the day, I try to do what is best for the football club and for Michael, as with any player.
"I will try to always get a player to sustain his fitness and sustain his availability for the team, and if that means not starting him, if that means pulling him off with 20 minutes to go and that gets him up to the mark we are looking for, then that is what I will do."
Johnson is facing ankle surgery and Blues boss Dave Moyes said: "He is having an ankle operation on Monday. He will be out for probably three to four weeks.
"It is a big blow for Everton. We have known for a wee while he has had a problem with his ankle, and he has also been carrying a groin injury, which kept him out recently.
"With the international break - unfortunately for England - it is probably the best time to get his ankle sorted now.
"It's something we have known about for a week or two.
"We just know he has got a problem and Andy wants it sorted, so we have to get that done."