Ellis scored a diving header on the hour to give the Wanderers a share of the spoils and in turn put an end to a disasterous run which had blighted Jimmy Phillips side prior to the Christmas break.
Striker Victor Anichebe hit the woodwork for Everton in the 13th minute after heading a dangerous cross by Stephen Wynne onto the post, and this was quickly followed by a shot from distance courtesy of experienced midfielder Lee Carsley.
On 24 minutes Carsley turned provider for the opening goal as it was his cross which set up Gary Naysmith to head the ball comfortably past Bolton goalkeeper Chris Howarth.
French forward Bedi Buval almost forced a reply for Bolton shortly before the break but Toffees goalkeeper Iain Turner was alert to the danger posed by the teenage front man.
The visitors came back into the game after the interval courtesy of Ellis who took advantage of some slack Everton defending in the area to put the ball past keeper Turner with a diving header.
Substitute Leslie Thompson nearly forced Bolton into the lead later on in the half but the Londoner was unable to keep his balance and therefore missed the chance to net a winner.
Bolton Reserves: Chris Howarth, Bradley Hill, Scott Jamieson, Dale Whitehead, Jarostaw Fojut, Mark Ellis, James Sinclair, Robert Sissons, Bedi Buval, Johann Smith, Sean Mountford (Leslie Thompson)
Subs Not Used: Przemyslaw Kazimierzczak, Matthew Cassidy, Mark Charlesworth, Danny Stott
Everton Reserves: Iain Turner, Stephen Wynne, Laurence Wilson, Mark Hughes, Patrick Boyle, James Harris (Bjarni Vidarsson), Christian Sergeant, Lee Carsley (Scott Phelan), Victor Anichebe, Li Tie, Gary Naysmith
Subs Not Used: Jamie Jones, Sean Wright, Lee Molyneux
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