In the election held in the House, Lobo polled 21 votes, while Fernandes bagged 15.
While Speaker Pramod Sawant did not vote, two MLAs - Churchill Alemao (NCP) and Francis Silveira (Congress) - were not present in the assembly at the time of the election.
The coastal state has a 40-member House and one MLA resigned days after assembly poll results were announced two weeks ago.
Chief Minister Manohar Parrikar escorted Lobo to his chair after he was declared elected.
Parrikar congratulated the MLA from Calangute on assuming responsibility of an important post.
In his speech, Lobo described Parrikar as a "visionary leader".
"I will always be with Parrikar due to his vision for Goa. Parrikar quit as Defence Minister for the sake of Goa. People of Goa know why he came (back as chief minister). There are pending issues which need to be settled," he said.