But Wheater made amends within moments, rising high to head home from Fabio Rochemback's corner.
BBC: SPORT | Football | Premiership | Middlesbrough 3-1 Fulham
O'Neil follows David Wheater out of the Riverside, with the defender joining Bolton last week.
Nicky Butt was then only inches off target with a 20-yard free-kick after David Wheater had fouled Guthrie.
David Wheater cleared a Manucho header off the line before Marlon King slotted in to secure Boro's win.
And in the final 10 minutes, Bolton debutant David Wheater shot just wide.
Martins then had an effort deflected just off target via Wheater as the game finally showed signs of opening up.
David Wheater volleyed in for Boro late on but the goal was disallowed for pushing, and Justin Hoyte hit the post.
Bolton defender David Wheater had to rely on his goalkeeper, Adam Bogdan, to spare his blushes when he sliced an early clearance.
Jones missed a cross and needed Wheater to clear Manucho's header off the line, which did nothing for the home side's nerves.
It was thought that Premier League vultures would swoop for the club's assets such as David Wheater, Tuncay and the injured Stewart Downing.
Wheater made a complete hash of clearing Carlos Bocanegra's hopeful punt forward and Davies nipped in between defender and keeper to volley home.
BBC: SPORT | Football | Premiership | Middlesbrough 3-1 Fulham
Kalou got his second when his low strike deflected off David Wheater before Frank Lampard's diving header rounded off a superb Chelsea breakaway.
Wheater had a great chance to break the deadlock in the seventh minute, but his free header from Julio Arca's corner bounced tamely wide.
BBC: SPORT | Football | Premiership | Middlesbrough 3-1 Fulham
Malouda's exquisite cut-back found Kalou and, with everything going Chelsea's way, the striker's low shot diverted off Wheater to leave keeper Ross Turnbull no chance.
Boro led 1-0 at half-time through David Wheater's 44th-minute goal but Marouane Fellaini and Louis Saha scored to give Everton a showdown against Manchester United.
Boro's academy has unearthed several notable homegrown players in recent years, including England international Stewart Downing, and under-21 stars Andrew Taylor, Lee Cattermole and David Wheater.
BBC: SPORT | Football | My Club | Middlesbrough | Boro chief rejects Brooking claim
Wheater, who would have been out of contract in June, came through the ranks at Boro and made his debut for the club in March 2005.
Meanwhile, the club is waiting for news on the condition of centre-back Chris Riggott, who hobbled off and was replaced by David Wheater in Sunday's game.
The former Eintracht Freising centre-back arrives at the Riverside following the departure of former England Under-21 international defender David Wheater to Bolton Wanderers earlier this month.
David Wheater, called up by England earlier in the week, came closest to giving the home side the lead but the impressive Carroll reacted quickly to clear.
Wheater headed wide at the other end when Duke failed to punch a Stewart Downing free-kick away before an escape for the home side at the other end.
Former Crystal Palace man Moses then saw a powerful effort blocked by Wheater, before his Wigan team-mate Gomez tested Jaaskelainen with three fierce shots from outside the area.
Taylor crossed from the left and Cresswell outmuscled David Wheater to land a powerful header, which Danny Coyne got a hand to, but was unable to keep out.
Villa then enjoyed a lengthy period of possession but the home defence, boosted by the return of David Wheater, who was playing despite requiring knee surgery, held firm.
Petrov screwed a shot wide, Ashley Young was foiled when through on goal, Wheater cleared off the line from an Agbonlahor header and Jones saved well from the same man.
Tottenham were not as fluid after the break, and Boro came close to equalising in the 47th minute only for the ubiquitous Lennon to clear David Wheater's goal-bound header off the line.
But, despite the open nature of the game, the changes brought United no closer to a breakthrough, with their attacks regularly thwarted by the excellent Bolton central defensive pair of Cahill and David Wheater.
Since then a number of players the club brought through its academy such as Stewart Downing, Lee Cattermole, David Wheater and James Morrison have left, and Hasselbaink believes the club have paid the price for selling their home-grown stars.
Either side could have grabbed a winner in the last few minutes of the match, first when 19-year-old Wigan striker McManaman forced another athletic stop from flying Finn Jaaskelainen before Wheater smashed a loose ball in the area inches wide of the Wigan goal.
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