The new format is part of the revamped Academy system set up under the Premier League's Elite Player Performance Plan.
Boro will split their game programme between Rockliffe Park and the Riverside Stadium with the opening game taking place in glorious sunshine at the club's training HQ.
Jamie Clapham's side began the game strongly and Jake Fowler went close after a flowing move involving Bruno Pilatos and Curtis Edwards
Skipper Matty Dolan blasted a ferocious free-kick into wall after foul on Edwards after 17 minutes, but it wasn't long before the same player broke the deadlock with a stunning goal.
After a patient, controlled build-up, Dolan picked the ball up 30 yards out and took just one touch before hitting a screamer into the top, right-hand corner on 22 minutes.
The advantage was doubled three minutes later as Wilson Kneeshaw prodded home the rebound after Ryan Brobbel's powerful shot was spilled.
Bayan Fenwick went close for the visitors with a 25 yard free-kick, but Boro were in cruise control by now, passing them ball unerringly on an immaculate playing surface, with the visitors not quite knowing what had hit them.
Another fantastic strike to one to rival Dolan's opener made it 3-0 to Boro on 34 minutes.
A fine pass from Joe Bennett, playing his first game since returning to pre-season training, found Brobbel, who unleashed a fine effort that curled into the top left-hand corner of the goal.
Jarrett Rivers replaced Kyle Oliver at half-time and Palace soon showed they were eager to stop the Boro tide and make a game of it.
But 11 minutes into the second half the visitors found themselves 4-0 down. Kneeshaw surged into the box and sneaked over a cross crossed despite being smothered by Palace defenders and sub Rivers tucked home from close range.
There was a rare touch for Connor Ripley as he firmly held Fenwick's swirling effort on 62 minutes, before Brobbel's header was then brilliantly saved by Ross Fitzsimons after an excellent Kneeshaw cross, the Palace keeper then performing heroics with four minutes remaining to turn round Wyke's long-range stinger. In between Fitzsimons's saves Fenwick went on a good run through the middle, but wasted a chance to set up Riese Allassanni when slightly over-hitting his through ball.
The game ended 4-0 after a highly-impressive Boro performance.
Boro: Ripley; Pilatos, Burgess, Jackson, Bennett, Oliver (Rivers 46), Dolan (Capt) (Waters 76), Edwards, Brobbel, Kneeshaw (Wyke 69), Fowler. Unused subs: Montgomery (gk); Sirrell.
Palace: Fitzsimons, Akaruka (Banton 46), Chambers, Taylor, Holland, Wynter, Fenwick, Boateng, Woodley (Sow 46), Allassanni, Daniel. Unused subs: Gregory (gk), Gray, Kai Kai.
Man of the Match: Ryan Brobbel