Son of the Chian merchant Antonis Benakis. He studied commerce in London. He initially engaged in trade in Ermoupolis but quickly left for Egypt, where he worked for the trading house of Choremis-Mellor. He later became a partner of Horemie and they established a new company. He was president of the Greek Community of Alexandria for 10 years (1901-11). He acquired great wealth and social power. He founded the Benakion Orphanage for Girls and the Benakion Soup Kitchen.

In 1910 he returned and settled in Athens. He became involved in politics and was elected as a deputy in Attikovoiotia, in the 1st Revisionary Parliament (1910-11) and in the 2nd in 1911 and again as a deputy in 1912-15. He was Minister of Agriculture, Trade and Industry in the government of El. He served as Minister of Agriculture and Industry in Greece in El. Venizelos. In 1914 he was elected Mayor of Athens but resigned for political reasons the following year. His stately grand house became the centre of the Liberal Party. In 1920, he accompanied Eleftherios in his election campaign. Venizelos to France (self-exiled).

He returned from self-exile in 1924. From then on he became a private artist and was involved in the creation of public works. He spent huge sums of money on the establishment of refugee hospitals, refugee employment factories (carpet factory, handicrafts, etc.). It supported with funds the Air Defence Organisation, the patriotic care foundation, the Kifissia community school, the National Gallery. In 1927 he was declared a national benefactor. Donor to the Hellenic American College of Athens, the Red Cross Hospital, the Municipal First Aid Station, the Children’s Asylum of Kifissia. And the list goes on with the Benaki Phytopathological Institute, the Benaki Library, collections of antiquities and folklore and so many other benefits to the Greek people.

The state honoured him with the Superior Brigadier of the Order of the Saviour and with the Gold Medal of the Academy of Athens. He was buried at public expense.