A 50th minute free kick from midfielder Laurence Wilson ensured that the points went back to Merseyside but the win came at a price for the Toffees as midfielder Li Tie suffered a relapse in his attempts to come back from a long term injury and was substituted shortly before the break.
Ex-Toffees full back Neil McDonald saw his Bolton side create a number of chances with Senegal international Khalilou Fadiga having two good efforts, the second of which was spectacularly tipped away by Everton goalkeeper Iain Turner.
The Merseysiders had chances themselves and where unlucky not to have taken the lead before the break when striker James Vaughan saw his shot cleared away by Jason Talbot who was returning to the Bolton side following a spell out on loan with Mansfield Town.
Wanderers pressed for an equaliser in the closing stages of the game but Bolton striker Bedi Buval was unable to find his way past the unflappable Turner in the Everton goal.
BOLTON RESERVES: Andy Oakes, Ricky Shakes, Jason Talbot, Florent Laville, Charlie Comyn-Platt (Jaroslaw Fojut), Dale Whitehead, Blessing Kaku, Khalilou Fadiga, Ricardo Vaz-Te, Bedi Buval, Henrik Pedersen
SUBS NOT USED: Prze Kazimierczak (GK), Reda Kribib, Rhys Powell, Robert Sissons
EVERTON RESERVES: Iain Turner, Stephen Wynne, Daniel Fox, Patrick Boyle, Anthony Gerrard, James Harris, Christian Seargant (James Vaughan), Li Tie (Paul Hopkins), Nick Chadwick, Bjarni Vidarsson, Laurence Wilson
SUBS FROM: Craig Gallagher (GK), Victor Anichebe, Sean Wright