Shepherd, who scored both of Cornwall's tries in their County Championship win over Lancashire, scored England's second try and kicked four conversions.
Hilton scored England's third try as they twice overturned deficits to win.
The victory added to a 28-16 win over club side CSM Bucuresti that England registered in their opening game.
Cornwall duo Matt Shepherd and Ben Hilton scored tries as England Counties ended their tour of Romania with a 28-20 win over Romania 'A'.