The 23-year-old centre-back had been sidelined since April by a long-term injury that required surgery, having originally signed a new five-year contract with the club earlier this month after attracting interest from Manchester United and Tottenham.
He started alongside James Tarkowski, Jake O'Brien, Adam Aznou and Merlin Rohl in a back five, with Everton preparing for their Premier League opener against Crystal Palace in late August.
Everton believed they had taken the lead midway through the first half when Rohl's low ball into the box found Thierno Barry, who finished from close range, only for the effort to be ruled out for offside. It was the closest the visitors came to breaking the deadlock in a first half in which David Moyes' side gradually grew into the contest after a quieter opening period.
Five changes at the break brought on Tom King, Michael Keane, Kiernan Dewsbury-Hall, Vitalii Mykolenko and Tyrique George, with Mykolenko returning to the squad having been given time off for the birth of his second child. Beto had the best opportunity of the second half when Mykolenko's chipped ball found him behind the Bolton defence, but the striker could only shift the ball onto his favoured right foot before firing wide of the target.
Five Everton academy players earned minutes during the closing stages, with Harvey Foster, who scored for the club last week in Dundee, joined by Braiden Graham, Malik Olayiwola, George Finney and Eli Campbell as Moyes continued to run the rule over his younger options. Neither side could find a breakthrough as Bolton's defence held firm to secure the stalemate.
Everton return to pre-season action on Tuesday against Stoke City at the Bet365 Stadium, with Moyes still waiting for further reinforcements to bolster a squad that has seen limited fresh recruitment so far this summer.
New signing Hayden Hackney was again absent from the matchday squad, while winger Tyler Dibling missed out with a minor knock, though both are expected to be available against Stoke.