The win, coupled with Tottenham's loss at Chelsea, means fourth-placed Arsenal head to Wembley this weekend four points adrift of their local rivals.
"It is a big motivation," Emery told reporters.
"We need to take the opportunity like today, these three points. After we can have and get an opportunity like Saturday.
"They are still ahead of us in the table, and it's difficult to win there, but it's a good test."
Mkhitaryan and Ozil both put themselves in contention to start the derby with a goal apiece against Bournemouth, but Emery refused to be drawn on whether the pair had done enough to feature in his tactical plans for the weekend.
"I'm going to watch the match back, and Tottenham's, and after that I will decide our gameplan for Saturday with every player," he added.
"If we can play with big performance I want every player to help us with this decision."
(Reporting by Hardik Vyas in Bengaluru; Editing by Amlan Chakraborty)
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