Former United favourites Peter Beardsley and Lee Clark faced each other on the touchline as Rob Elliot continued his comeback in the behind-closed-doors game.
But the Scottish Premiership outfit - who played against Gateshead on Wednesday as part of a mini tour of the North East - came out on top on a bitterly cold afternoon.
There were few opportunities in the opening 25 minutes but the visitors broke the deadlock through Adam Frizzell, who fired home with a low shot.
And ten minutes later, they doubled their lead when defender Scott Boyd finished expertly after Newcastle failed to clear from a corner.
In the 44th minute, Yasin Ben El-Mhanni almost pulled one back after a superb solo run, but curled his shot just wide. Then the same player had an effort blocked after great work from Tom Heardman.
At the beginning of the second half, Newcastle did half the deficit through a trialist but Kilmarnock continued to have the better of the chances and Elliot made a fantastic save to deny former Scotland international Kris Boyd from close range.
He also dealt well with an acrobatic effort from Frizzell, but could no nothing in the dying seconds to prevent Dean Hawkshaw's deflected effort from finding the net.
Callum Roberts and Sean Longstaff, who joined Kilmarnock on loan from Newcastle earlier this week, both played a half for their new club.
Newcastle United Under-23s: Rob Elliot, Michael Newberry, Stuart Findlay, Curtis Good, Adam Wilson (Lewis Cass 46), Jack Hunter, Yasin Ben El-Mhanni, Daniel Barlaser, Liam Smith (Jamie Holmes 46), Dan Ward (Trialist 46), Tom Heardman (Trialist 46).