The second leg failed to match the fast start of the first leg, which saw two goals in the opening 10 minutes, though that was solely down to the raising of the assistant’s flag.
Fares Chaibi, the scorer of the opener in Brussels seven days ago, had visibly strayed beyond the last man Kevin Mac Allister before slotting home, and as protocol, it was only after the move had played out that the officials intervened.
That was just the start of a frustrating half for the Eagles, who were edged in terms of possession and forced to play on the counter. In one such instance, Omar Marmoush showed his irritation, gesturing to the home support inside the Deutsche Bank Park to get behind their team, then it took until first-period stoppage time for the hosts to register a shot on target - a Chaibi free-kick tipped over the bar by Anthony Moris.
This left Dino Topmoller and his troops to regroup. However, before they could enact their second-half plan, a sucker punch from Union saw them snatch the lead for the first time in the tie.
Two minutes after the restart Mohamed Amoura teed up Cameron Puertas on the edge of the area, allowing the midfielder to curl beyond Kevin Trapp into the bottom left corner - his team’s first strike on away soil in UEFA competition this campaign.
Amoura almost instantly added another with Frankfurt still stunned from the first, had it not been for an excellent last-ditch tackle from Robin Koch.
A mighty change of attitude was needed for Frankfurt, but in truth, it came too late. It remained one-way traffic towards Trapp’s goal and the punishing blow subsequently came with 10 minutes to go, as substitute Dennis Eckert Ayensa - back in his homeland - received the ball from a corner and blasted home from a tight angle.
Then, out of nowhere Eric Junior Dina Ebimbe, pulled one back for the hosts, also converting from a corner at the opposite end of the field, but in the few frantic minutes that remained they were unable to claw it back.
The tie ended 4-3 on aggregate, with the Belgians taking their place in the hat for the round of 16.
Flashscore Man of the Match: Cameron Puertas (Royale Union SG)
Other late Conference League results:
Ferencvaros 0 Olympiacos 1 (Olympiacos progress on aggregate)
Legia 0 Molde 3 (Molde progress on aggregate)
Slovan Bratislava 0 Sturm Graz 1 (Sturm Graz progress on aggregate)
