The reigning champions came from behind in the final 20 minutes at home to triumph 2-1 in the first leg thanks to goals from Carlos Bacca and Denis Suarez.
"The reality of the tie is this, Zenit is a great team and there will be a different game [in Russia] but we will compete equally," Emery told Sevilla's website.
But Emery made two changes at the break, replacing Vicente Iborra and Coke with Stephane M'Bia and Suarez respectively, which saw the hosts take control.
"The idea was to find a new way... not that in the first half Iborra and Coke were not good, but we changed the offensive aspects," the 43-year-old coach said.
Emery added: "Not the best but not the worst result. I think justice has reflected a little what is a tie between two teams that compete with their qualities. The first half they have proven to be a winning team and racing.
"We have identified [the problems] and 0-1 has made us rethink how the game was and how we could find a better way."
