Two goals in as many minutes midway through the first half put paid to Glentoran's European ambitions for this year.
With the sides tied at a goal apiece following last week's clash at The Oval it was all to play for but The New Saints seized the initiative with less than half-an-hour on the clock.
The first came on 26 minutes when Declan McManus fired past Dayle Coleing from the spot, awarded after the Glentoran keeper was adjudged to have impeded Jordan Williams.
Then, around sixty seconds later, Leo Smith - who scored in the first leg - struck again after he made the most of a defensive mix-up between Gael Bigirimana and Patrick McClean.
And there was almost a third on the half-hour only for Williams to scuff an effort against an upright.
The Glens did attempt to fight back, coming close before the break through when the home keeper just about tipped the ball away from Robbie McDaid while Seanan Clucas fired over from a good position.
After the break chances came through Jamie McDonagh and McClean, albeit both saved by Paul Harrison.
Then, later in the game, Ben Cushnie caused trouble for the home defence while McDaid sent a stoppage time header just over.
The New Saints: Harrison, Marriott, K. Davies. Astles, Routledge, McManus, Cieślewicz, J. Williams, Clark, Smith, D. Davies subs Roberts (not used), Ebbe (replaced K. Davies 75), Robles (replaced J. Williams 67), Canavan (not used), Daykin (not used), T. Williams (not used), Rees (replaced McManus 87), Cornish (not used)
Glentoran: Coleing, Kane, McCullough, Bigirimana, Marshall, R. Donnelly, McDaid, McClean, Clucas, Marron, McMenamin subs Morris (not used), Glendinning (not used), McDonagh (replaced R. Donnelly 67), Mitchell (replaced Clucas 57), Stewart (not used), Smith (replaced Marron 67), Cushnie (replaced Bigirimana 81), Wightman (not used)