Wivenhoe took a three nil lead into half time with strikes from Ross James, Sam Mead and Tim Dennis. In the second half the visitors got one back before Konnor Oughton was fouled for a penalty which was converted by Jack Mead.
Wivenhoe have won their last five games at the Blackstone Stadium, scoring 22 goals and conceding just four.
The Dragons will play Little Oakley away in the next round of the First Division Knock Out Cup.