The pontiff made the announcement on Nov. 3 in Rome.
He succeeds Bishop Ignatius Menezes (76) who has been on the post since 1979.
Fr. D'Souza was born in 1954 in Agra.
He was ordained a priest for the Lucknow diocese in 1982.
He is presently the chancellor Bareilly diocese.
Fr. D’Souza holds a doctorate in canon law from the Pontifical Urban University in Rome.
The Ajmer diocese is a suffragan of the Agra archdiocese.
The diocese has 10 parishes served by 43 diocesan priests, 21 religious brothers, 402 sisters and 23 major seminarians.