The former world number one, who dropped out of the top 10 for the first time in three years after failing to get past the first round of the US Open and is now ranked 11th, is still searching for her first title of the season.
The 22-year-old will now play either Kaia Kanepi of Estonia after she beat American Varvara Lepchenko 6-4 2-6 6-4 in their semi-final.
Saturday's championship match is just the second final the Dane has reached in 2012, having finished as runner-up in Copenhagen back in April. She has not lifted a trophy since New Haven in August last year, the last of six titles she won in 2011.
Wozniacki was knocked out in the first round in her only two previous appearances in Seoul and has not visited the South Korean capital since 2007, but her form at this year's event has been encouraging.
Having eased through her first three matches without dropping a set, she appeared to be cruising to another comfortable victory against Makarova, taking the first set for the loss of just one game.
But an early break in the second for Makarova handed the Russian the ascendency and she went on to force a deciding set.
In the third, Wozniacki had to work extremely hard to battle through and take it 6-4, but the Dane showed real composure and resilience in doing so.
It was an encouraging win for the Dane, who was absolutely delighted as she celebrated the victory in the Olympic Park Tennis Centre.