She felt a pain in her side.

Literal

[topic-は] side [in-に] pain [object-を] felt.

わき腹 ('side of the abdomen, flank') is a compound of わき ('side') and 腹 ('belly') — a body-part word more anatomical than 横腹 (its near-synonym). The verb 感じる ('to feel') takes を for the sensation experienced, and に for the location where it's felt. This に-marking of body location with sensation verbs is a very productive pattern: 頭に痛みを感じる ('feel a pain in one's head'), 胸に違和感を感じる ('feel discomfort in one's chest').