McClaren, expected to be named as Sven-Goran Eriksson's successor by the end of the week, made nine changes to the Middlesbrough team that drew at Manchester United 48 hours earlier.
And his young, inexperienced squad - including seven academy starlets - were good value for a point that reduced Bolton's chances of even qualifying for the Intertoto Cup.
One of those rookies, Adam Johnson, netted his first senior goal as Boro, playing their 63rd game of the campaign, almost won at Bolton in the top-fight for the first time in 56 years.
However, Portuguese prospect Ricardo Vaz Te spared Sam Allardyce's blushes with a flying header from Jay-Jay Okocha's cross.
It was Vaz Te's second Premiership goal following a recent header in the home win over Charlton - Bolton's solitary victory in nine outings.
On that occasion Allardyce won his personal duel with one-time England managerial candidate Alan Curbishley.
But Big Sam - who has already conceded he's out of the race to succeed Sven - couldn't do the same to McClaren.
It might have been different had Bolton taken their early opportunities as the visitors new look line-up took time to gel.
Vaz Te should have scored within 75 seconds after being freed by Okocha's first-time crossfield pass. Instead, he was foiled by Boro's third choice goalkeeper Ross Turnbull.
Kevin Nolan almost flicked Bolton in front from close range after four minutes following a Henrik Pedersen centre. Once more Turnbull came to Boro's rescue.
Vaz Te was booked for a blatant dive while Yakubu's elusive search for a goal goes on after a header midway through the first period from Malcolm Christie's cross was saved by Jussi Jaaskelainen.
Allardyce was then left shaking his head as Hidetoshi Nakata blazed over after good approach play by Nolan and Vaz Te.
Bolton had a scare when Doriva stole in goal side of Nicky Hunt and his left-foot effort wasn't too far wide.
Two minutes after the restart Boro silenced most of Bolton's lowest Premiership crowd of the season. Johnson cut in from the left wing, waltzed past Hunt with ease, and fired in right footed, though his effort deflected off the shin of Tal Ben-Haim.
Unfortunately for Middlesbrough they were unable to consolidate their advantage. Ivan Campo's acrobatic effort missed the target but there was nothing wrong with the direction as Vaz Te headed in from eight yards.
That should have been the signal for Bolton to win the game but despite pressure they couldn't force a winner. Indeed, Boro might have won it in the 72nd minute.
Jaaskelainen dropped a Franck Queudrue shot but Ugo Ehiogu put the rebound wide off the post.