Having returned from Vietnam with a 4-2 advantage heading into the second leg, hosts Kitchee were strongly fancied to advance to the last four heading into the clash.
And Jose Molina's men managed to achieve their goal, but only after being given a real fright by the visiting side.
Kitchee, who were thumped 6-2 by a Zlatan Ibrahimovic-inspired Paris Saint-Germain in a friendly last month, fell behind to Suleiman Oladoja's first-half strike, but were able to hold on to their 4-3 aggregate lead.
Last week's opening leg was Ninh Binh's first competitive outing since May after controversially withdrawing from V.League 1 but the visitors showed few signs of rustiness on Tuesday.
Kitchee's Jordi Tarres also hit the bar late on, while visiting skipper Shim Un-seob saw red in stoppage time after receiving a second caution.
