Already boasting a 3-1 lead from last week's opening leg, Rovers only needed to avoid a significant defeat in North Macedonia to set up a meeting with Azerbaijan's Qarabag.
But instead they advanced with a 2-1 win, with goals coming from Rory Gaffney and Aidomo Emakhu.
Shkupi had put Shamrock under plenty of pressure in the first half though both Gaffney and Richie Towell threatened on the break.
After a slow start to the second half from the visitors, Gaffney scored with their first opportunity since the restart with 65 minutes gone, with his shot picking up a deflection to beat the goalkeeper.
Substitute Emakhu then essentially settled it with six minutes left after being teed up by Graham Burke, though there was still time for Sundat Adetunji to pull one back in stoppage time.
While the Europa League is still in reach, the win means Shamrock are assured of Europa Conference League football at least.