On April 4, 1960, Rakotomalala was appointed Archbishop of Tananarive by Pope John XXIII. He received his episcopal consecration on the following May 8 from Pope John himself, with Bishops Napoléon-Alexandre Labrie, CIM and Fulton John Sheen serving as co-consecrators, in St. Peter's Basilica. Rakotomalala later attended the Second Vatican Council from 1962 to 1965, and sat on the Council's Central Preparatory Commission.
Pope Paul VI created him Cardinal Priest of S. Marie Consolatrice al Tiburtino in the consistory of April 28, 1969. Rakotomalala was the first cardinal to hail from Madagascar as well.
The Cardinal died in Tananarive, at the age of 62. He is buried in the metropolitan cathedral of Tananarive, now called Antananarivo.