A last-gasp goal from Virgiliu Postolachi earned the French champions victory at the National Stadium, though, leaving them with four points from their three fixtures in the friendly competition, while last season's La Liga runners-up have one point from one game fewer.
With a little over half an hour played PSG bagged their first of the contest, though, as Nkunku tucked the ball over the line from close range after a deflected shot landed in his path.
If not for a Kevin Rimane clearance off the line the match would have been all square at the break, but it was the Parisians who would score the game's second goal to give themselves some breathing space.
Tim Weah twice threatened to score without actually doing so, but Diaby had better luck as he followed up his earlier shot against the bar with a left-footed finish into the bottom corner.
It was game on again with 15 minutes left to play in the Far East when Victor Mollejo scrambled the ball over the line after PSG failed to clear a corner.
Antoine Bernede then sent the ball into his own net as he attempted to block a cross towards the front post, but PSG would regain their lead through an impressive Postolachi strike in added time - the youngster turning on the edge of the box and curling the ball into the top corner.
PARIS SAINT-GERMAIN FIRST-HALF XI: Trapp, Rimane, Nsoki, Diarra, Kurzawa, Dagba, Verratti, Lo Celso, Rabiot, Nkunku, Di Maria
PARIS SAINT-GERMAIN SECOND-HALF XI: Trapp, Georgen (Postolachi 51'), Loic Mbe Soh (Bahabeck 60'), Sissako, Weah, Bernede, Toufiqui, Adli, Diaby, Fressange, Zagre
ATLETICO MADRID XI: Adan, Juanfran (Munoz 64'), Toni Moya, Montero, Olabe, Thomas (Munoz 46'), Rodri (Mollejo 64'), Mikel Carro, Correa (Pinchi 64'), Gameiro (Solano 64'), Vietto (Moreno 64')