After losing 2-0 away in Malta in the first leg, the Luxembourgish side had a mountain to climb at home on Wednesday.
Although Hadji scored a brace, putting the home side ahead in the 38th and 84th minutes, Gzira United's Wilkson grabbed a goal just minutes before the final whistle, thus securing the Maltese team's place in the next round at the expense of Dudelange.
On Tuesday, Swift Hesperange progressed to the third round following a resounding win over Welsh champions New Saints.