Missing out on the Brazilian is a fresh blow for Arsene Wenger, who has missed out on several targets this summer, and is currently caught up in the saga involving Liverpool's want-away striker Luis Suarez.
Bernard, 20, signs for the Ukranian side on a five-year deal, for a fee of £21.5million (€25m) and will be aiming to fill the void left by fellow Brazilian Fernandinho's move to Manchester City earlier this summer.
Missed out: Bernard was impressive in Atletico Mineiro's Copa Libertadores win, and has five caps for Brazil
The move comes as a surprise as it was thought that the youngster, who can play behind the striker or on the wing, was favouring a move to Portugal, being persuaded by Brazil teammate and former Porto player Hulk.
Speaking to O Jogo, Bernard's father said: 'Hulk has convinced Bernard that Porto would be better for him at this stage of his career.
'Porto would be a better move for his career. It would be a dream of mine to see him playing for them.'
Arsenal were also vying for his signature, especially after the departure of Gervinho to Roma has left a shortage of wingers at the north London club.
Wenger meanwhile, has said that the move for Uruguayan stiker is 'on standby' after the 26-year-old told his club he wanted to play Champions League football.
Reds boss Brendan Rodgers has criticised the striker for showing a complete 'lack of respect' and has ordered him to train by himself for the time being.