Roberto Mancini's side headed into the Everton clash on the back of five consecutive victories but an impressive first-half display from the Toffees was enough to secure the three points.
The diminutive South African Pienaar bagged the first after 36 minutes with a curled free-kick before Saha made it two on the stroke of half-time.
Everton piled the pressure on their big-spending opponents from the first whistle and might have taken the lead after 26 minutes but Shay Given was equal to Diniyar Bilyaletdinov's left-footed half-volley.
But the home fans didn't have to wait much longer for their opening goal with Pienaar's measured 20-yard free-kick doing the damage.
Former Manchester United frontman Saha was brought down by Pablo Zabaleta and Pienaar curled the free-kick through a hole in the wall and past Given.
And on the stroke of half-time Saha made it two from the spot. Micah Richards was adjudged to have pulled Saha's shirt and the Frenchman made no mistake from the spot.
Tim Cahill should have extended Everton's lead on 46 minutes when he headed just wide from Phil Neville's long throw.
City almost scored from an impressive counter-attacking move after Shaun Wright-Phillips picked up the ball from an Everton corner and started a move that ended up with Craig Bellamy firing wide.
Bellamy then sent Gareth Barry scampering clear on 74 minutes but his cross from the left was comfortably taken by Tim Howard.
Everton might have had three when Marouane Fellaini's thumping header was touched on to the crossbar by Given.
And the dominant Toffees hit the woodwork again late on when Cahill headed against the post from Leighton Baines' cross.