First, note that many tools of the Stone Age were not stone. Many tools were made of wood, bone, horn, and antler, and these materials continued to be used for tools well into the Iron Age (in some cases, into modern times).

Second, stone tools continued in use into the Bronze Age, and Iron Age, and some are still in use today.

1. In some cases, stone is a very good material for the tool. For some of these tools, stone is still used today. Sometimes, synthetic stone is used for the modern version, and sometimes natural stone. Examples of stones tools still in use include grindstones, whetstones, mortars, pizza stones and other stone cookware, and fire-lighters. There is also small-scale use of obsidian/glass blades for "real" use (e.g., scalpels for microsurgery). In some cases, the tool itself has largely become obsolete (e.g., a flintlock mechanism for guns).

2. In some other cases, stone works well, and is better than bronze, and sometimes better than iron, but the usual modern version is hardened steel. For example, stone hammers and anvils were used in traditional African ironworking well into the 20th century (even today, stone anvils are still used, but hammers are commonly steel).

3. In other cases, both stone and metal versions of tools were used. Often, the stone version was a cheaper alternative to metal, and the metal version was a longer-lasting (but more expensive) alternative to stone. Depending on the tool, the stone version might be better apart from durability. For example, stone blades (daggers, knives, etc.) and arrowheads were used into the Iron Age. Sling stones were used well into the Iron Age. For tools like this, the degree of replacement of the stone version by the bronze (or iron) version varied with the tool, and with the cost of the bronze/iron version. For many bladed tools, the bronze versions were preferred, and became the usual version in the late Bronze Age.

Further reading: Berit V. Eriksen (ed), Lithic Technology in Metal-Using Societies, Aarhus University Press (2010)