Clijsters completed the women's quarter-final line-up despite struggling early on against 49th-ranked Makarova's forehands down the line as the evening cool turned into a night chill.
The three-times U.S. Open champion roused herself to claim the first set tiebreak 7-3 and never again looked in danger as she cruised on to a last eight date with Pole Agnieszka Radwanska, who beat China's unseeded Peng Shuai 7-5 3-6 7-5.
"It's been tough," said Clijsters, who called for the trainer after she felt her hamstring tighten in the second set.
"In these last few matches, I always played players that I kind of never played against. It was always a little bit hard to kind of find that rhythm.
"I definitely felt a big improvement (tonight) compared to my previous match."
In Image: Supporters of Spain's Rafael Nadal cheer him on during his fourth round match against Croatia's Marin Cilic at the Australian Open tennis championships in Melbourne, Australia, Monday, Jan. 24, 2011.
Full Coverage: Australian Open 2011