Barcelona confirmed the signing of Croatian international Rakitic on Tuesday, with Denis Suarez moving in the opposite direction on a two-year loan deal.
Rakitic made 149 appearances in three years at Sevilla, and Emery posted on his personal blog: "It was an honour to coach a player like him. He's an example on and off the field.
"I want to thank Ivan for his commitment, professionalism and Sevillismo.
"Good luck at Barcelona."
Although clearly disappointed at the loss of such an important player, Emery was also keen to stress the importance of Sevilla's future rather than dwelling on the past.
He said: "People leave but Sevilla will always be there.
"Sevilla are working to find another Rakitic. I want to welcome two young, hungry players, Suarez and Aleix Vidal."
Suarez is keen to impress at Sevilla and posted on his personal Twitter account: "I come to earn the respect of the fans."
Emery guided Sevilla to UEFA Europa League success and a fifth-placed finish in La Liga last season.
