A header from Filip Duricic gave Panathinaikos the lead just eight minutes after half‑time, reducing the aggregate margin to one and sending the raucous Olympiako Stadium into life.
Rangers keeper Jack Butland was tested repeatedly in the opening period and produced several critical saves to keep the Scottish side in control.
Within four minutes of coming on, substitute Djeidi Gassama restored Rangers' lead on aggregate, firing in the leveller within a minute of being introduced on the hour mark and proving yet again his credentials as an impact player off the bench.
His strike effectively sealed the outcome and quelled the threatening momentum building behind Panathinaikos' pressure.
Despite maintaining possession superiority and racking up more attempts on goal, Panathinaikos lacked clinical finishing throughout.
Rangers, though under siege for long spells, defended with determination and pragmatism to see the result through, marking a promising start for Russell Martin's tenure at Ibrox.
Next up, Rangers will face Viktoria Plzen, who overcame a 1-0 deficit to get past Swiss side Servette, winning 3-1 on the night.
The first leg is scheduled at Ibrox on either August 5th or 6th, with the return leg in early August. If they win that tie, they will enter the play‑off round, where potential opponents include big names such as Benfica, Club Brugge, Nice, Salzburg and Brann.
If they fall at that hurdle, they will drop into the Europa League play‑off round instead.