He moved to Israel in 1948 and continued his studies at the Hebrew University of Jerusalem and at École pratique des hautes études in Paris.

In 1959 he joined the teaching staff of the Hebrew University of Jerusalem, where he formed and headed the Russian Studies Department.

In 1970 Confino joined Tel Aviv University, and in 1971 he founded the Institute of Russian and Eastern Europe studies, which he headed until 1977.

Between 1980 and 1985 Confino served as a visiting professor at the universities of Stanford, Harvard, Duke, Chicago and some institutions in Europe.

Confino specialized in researching the history of Russia and the problems of Europe's agricultural comparative framework of the social structure, under different regimes, both past and present.