United's reserves were back to full strength after a handful of starlets linked up with the senior squad for the tour of Africa.
Cleverley opened the scoring on 28 minutes as he fired home a Fraizier Campbell pass; but the Scousers drew level before half-time as Nathan Eccleston drilled home an astonishing effort from 25-yards.
The Red Devils re-took the lead six minutes after half-time with Campbell once again the provider. His cross found Gray who tapped the ball home from only yards out.
Gary Ablett's men pulled level on 72 minutes as Jordi Brouwer beat Zieler - but United had the final laugh in a topsy-turvy contest as Drinkwater supplied a neat finish to a floating cross from Cleverley.
The win means United bring the Lancashire Senior Cup back to Old Trafford for the first time since 1969.
Full Time - Manchester United 3-2 Liverpool
Attendance - 606
Manchester United: Zieler, Gray, Eckersley, Cathcart, Chester, Simpson, Possebon (Drinkwater 46), Gibson, Campbell, Cleverley, Hewson (Evans 88). Unused subs: Derbyshire, Amos, Eikrem.
Liverpool: Bouzanis, Scott, Irwin, San Jose, Huth, Kelly, Lindfield, Eccleston (Amoo 83), Brouwer, Simon, Bruna (Kacaniklic 70). Unused subs: Hansen, Metcalf, Pepper.
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