Manchester United defender Wes Brown was also recalled, while Liverpool's Steven Gerrard returns after injury.
Rooney then struck the bar from Wes Brown's cross as United threatened to run riot.
The striker seemed certain to convert Wes Brown's low, powerful cross but the ball struck Kirkland and slowly dribbled goalwards.
Ferguson made a double change on the hour, sending on Carlos Tevez and Wes Brown for Berbatov and Gary Neville.
"People are aspiring to get into luxury brands earlier than ever before, " says Wes Brown , of market research firm Iceology.
Full-back Wes Brown said he had got just one hour's sleep, while Vidic admitted he had not even had as much as that.
Wes Brown was twice called into action at the other end to clear his lines as the Hammers showed plenty of willingness to attack.
England should have fallen two behind after Wes Brown's mistake left Fabiano clear and he was brought down by his Manchester United teammate Foster.
United's reshuffled defence, which saw substitute Owen Hargreaves come on at right-back and Wes Brown moved to centre-back, had coped well with Chelsea's threats.
Former Manchester City midfield man Elano split Wes Brown and Matthew Upson with a glorious pass and Nilmar arrived to direct a header beyond Foster.
Ferguson felt the free-kick from which John Terry scored should not have been awarded, and also felt Wes Brown was fouled as it went in.
As Boro regrouped United were indebted to some brave defensive play from Wes Brown, who first tackled Yakubu and then came across to block Stewart Downing's attempted cross.
BBC: SPORT | Football | Premiership | Man Utd 1-1 Middlesbrough
United have eight defenders out of action, with Nemanja Vidic (flu), Rio Ferdinand (calf), Wes Brown (hamstring), Gary Neville (groin), Rafael (shoulder) and Fabio da Silva (groin) are sidelined.
United romped to a 4-0 victory at lowly West Ham, but suffered more defensive problems as England internationals Gary Neville and Wes Brown joined an already lengthy injury list.
Instead, United clinched the win but not without a cost, with Wes Brown being forced off at half-time with a suspected leg injury and Evans now facing a suspension.
His list of injured defenders includes England internationals Gary Neville and Wes Brown, who both limped out of Saturday's game, plus longer-term defensive casualties Rio Ferdinand, John O'Shea and Jonny Evans.
With doubts over the fitness of Rio Ferdinand, and Wes Brown and Joleon Lescott ruled out through injury, Capello and assistant Franco Baldini managed to persuade Carragher into reversing his decision.
United defenders Rio Ferdinand, Patrice Evra and Wes Brown are already sidelined and it is unlikely Evans will be fit to face Tottenham in the FA Cup fourth round on Saturday.
But a goal from England international defender Wes Brown after 28 minutes gave 11-times cup winners Manchester United a 1-0 win, despite Crawley having much of the possession in the second half.
BBC: Crawley fans see narrow cup defeat at Manchester United
In addition, Wes Brown had to be substituted at half-time in the win over Wanderers because of a leg injury - but Ferguson hopes his injury problems will ease over the international break.
They were almost caught napping early on when Barry Bannan slid a ball inside right-back Wes Brown to find Stewart Downing and it needed centre-back Rio Ferdinand to come across and clear out the danger.
And another probing delivery from Baines should have brought a goal for Donovan but the man on loan from Los Angeles Galaxy failed to react when the ball bounced off Wes Brown six yards out.
Rooney and Alan Smith failed to fulfil defensive duties as Gregory Tafforeau raced forward and crossed for Acimovic, who stole between Wes Brown and Mikael Silvestre to fire high past Edwin van der Sar from 10 yards.
Beckford, who is a target for a number of leading clubs, took advantage of defensive indecision to latch on to a long ball from Jonny Howson and hold off Wes Brown before beating Tomasz Kuszczak from an acute angle.
Smalling is a real talent in the making, but he is inexperienced and, with Rio Ferdinand still out, you could now be looking at a United back four of Patrice Evra (if he's fit), Smalling, Wes Brown and John O'Shea.
United - with only one clean sheet to their name this season - fielded centre-halves Wes Brown and Jonny Evans - in for the injured Nemanja Vidic and Rio Ferdinand - but it was their front men who were the busier pairing.
His chances of being selected for Capello's squad for South Africa, which will be trimmed down to 23 players by 1 June, have been boosted because of doubts over the fitness of first-choice central defender Rio Ferdinand of Manchester United, as well as the absence of the injured Manchester City defender Joleon Lescott and United's Wes Brown.
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