She pulled the weeds in the garden.

Literal

She [topic-は] garden [possessive-の] weeds [object-を] pulled.

雑草を抜く ('to pull weeds') is the standard expression for weeding. 抜く means 'to pull out / extract' and is used for anything removed by pulling — weeds, teeth, hair, swords from scabbards. 雑草 ('weeds,' literally 'miscellaneous grass') is a straightforward Sino-Japanese compound.