The two subspecies of Speckled Cape tortoise (Homopus signatus signatus & H. s. cafer) are considered by most to be the smallest known tortoise species at under 5" as full grown adults. Some of the many Tent tortoise species of South Africa also remain very small as adults. The Egyptian tortoise (Testudo kleinmanni) is a very close also.
Yup Homopus signatus is the smallest species of tortoise at 8.5 to 9.5cm. The rest of the genus is small also, Homopus areolatus...10 to 12cm, Homopus boulengeri...9 to 11cm, Homopus femoralis...11 to 16cm and Homopus solus...9 to 10cm.
The Psammobates genus also has some small tortoises. Psammobates tentorius tentorius...9 to 13cm, Psammobates tentorius trimeni...10 to 15cm, Psammobates tentorius verroxii...10 to 15cm and Psammobates oculifera...11 to 13cm. Testudo kleinmanni is also small at 10 to 14cm as is Pyxis arachnoides...12 to 15cm and Pyxis planicauda...10 to 12cm.
Not the smallest, but... Kinixys natalensis is only supposed to grow to the 10-14cm range. Kinixys homeana and kinixys belliana are also supposed to stay below 17cm. They're all different types of hingebacks.