The Australian advanced to the last four with a 2-0 win over Lyubov Shulika of Ukraine.
Meares had to wait to discover her opponent as Guo Shuang of China drew level at 1-1 with Cuba's Lisandra Guerra Rodriguez. A decider was required, which Guo won.
Defending champion and six-time world sprint champion Pendleton advanced with a 2-0 best-of-three quarter-final win over Olga Panarina of Belarus.
She is poised to meet Kristina Vogel in the last four after the German beat Lithuania's Simona Krupeckaite 2-0.
Meanwhile, Laura Trott won her second event in the women's Omnium with victory in the elimination race. The result restored the 20-year-old world champion to the top of the standings.