The former world number one, who was knocked out in the first round in her only two previous appearances at the tournament, brushed aside the seventh seed to secure her place in the last four.
Wozniacki has yet to lose a set in Seoul this year, and she continued her impressive run with a hugely convincing performance against the Czech player.
"This is my first time back here in Seoul since 2007. Time goes quickly! But I'm happy to be here again," she said.
"The tournament has changed a lot since then, but the people are as nice and polite as always and it's really nice to be back."
It was a comprehensive victory for Makarova, who made light work of her opponent with a belligerent and unwavering display of power hitting from the back of the court.
On the other side of the draw, third seed Kaia Kanepi of Estonia overcame the challenge of Kiki Bertens of the Netherlands 6-4 6-4 in their quarter-final.
World number 16 Kanepi secured breaks of serve in both sets to seal her place in the last four, where she will next take on sixth seed Varvara Lepchenko.
The American recovered from a set down to beat Tamira Paszek of Austria 4-6 7-6(3) 6-4 to secure her progression.