Los Che accepted a €30 million (£25.9m) bid from the Premier League side on Monday, with the deal expected to be confirmed in the coming days.
The departure of the striker, who scored 28 goals in 42 appearances in all competitions last season, leaves Valencia with a sizeable void to fill in their attack but Djukic is remaining positive over the season ahead.
"Everyone here believes in this project," he told reporters. If we all come together we can achieve great things.
"Roberto has done great things for Valencia and we are grateful, but we are a big club who have seen big players leave before."
Valencia missed out on qualifying for next season's Champions League after finishing in fifth place last term under Ernesto Valverde and opted to appoint Djukic as first team coach in June after he spent two seasons with Valladolid.