The tiring Rooney gave way to Berbatov, while Shaun Wright-Phillips was the somewhat surprising replacement for Adebayor.
But Wright-Phillips wasted his chance to level with a weakly taken spot-kick, easily stopped by Nelson.
Chelsea won the game following second-half goals from Andriy Shevchenko and Shaun Wright-Phillips.
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Notts keeper Stuart Nelson then saved Bradley Wright-Phillips' penalty after Joe Ayinsah was fouled by Mike Edwards.
Wright-Phillips moved to Home Park in July 2009, but injury lay-offs limited his first-team appearances until this season.
Capello's other wide options include fit-again Aaron Lennon of Tottenham, Arsenal's Theo Walcott and Shaun Wright-Phillips of Manchester City.
Shaun Wright-Phillips set England on their way when his shot from the right went through keeper Mart Poom's legs.
He then set up Wright-Phillips, but his effort was too close to Howard.
Hayes made it 2-0 when he slotted home a low Bradley Wright-Phillips cross.
But it was City that started the strongest, with Micah Richards, playing at right-back, linking up dangerously with Shaun Wright-Phillips.
Crouch set up a great chance Shaun Wright-Phillips but his angled drive from 10 yards was straight at keeper Stipe Pletikosa.
Shaun Wright-Phillips doubled the first-leg advantage with a low finish from eight yards after he was put through by Patrick Vieira.
Winger Craig Noone and striker Bradley Wright-Phillips have both been linked with January moves away, as Argyle come under increasing financial pressure.
Chelsea's Shaun Wright-Phillips is the latest Premiership player to be accused of diving in order to get an opposition player sent off.
Wright-Phillips was accused of diving in Chelsea's 1-0 FA Cup quarter-final win on Wednesday and Newcastle defender Robbie Elliott was sent off.
Queens Park Rangers' Shaun Wright-Phillips, for instance, ignored the jubilation on his team's bench when he scored a late winner against Chelsea.
The former France international threaded his pass into the box for Wright-Phillips, who slid his shot past the long reach of Pantilimon.
Wright-Phillips then turned provider to cross for Tottenham's Crouch to bag his second in the 80th minute, his 20th goal in 37 internationals.
Capello could also consider a switch in formation, playing five in midfield, with Joe Cole or Shaun Wright-Phillips likely to come into contention.
Chelsea made a double switch with 17 minutes left, sending on Tal Ben Haim and Shaun Wright-Phillips for Ashley Cole and Joe Cole.
And he got the second Chelsea's blistering opening spell fully deserved after 20 minutes, but much of the credit must go to Shaun Wright-Phillips.
Booed and jeered off the pitch, McClaren had to act and he brought on Defoe and Beckham, with Gareth Barry and Wright-Phillips making way.
Before that it had been plain sailing for England, who got the start they wanted when Wright-Phillips' shot squirmed past Poom after only 11 minutes.
Zaza did even better to stop Robinho's first-time shot after good work by Stephen Ireland, while Wright-Phillips was horribly off-target following another sublime Elano through-ball.
England winger Wright-Phillips got on the scoresheet four minutes later before Rosicky pulled one back (88) and defender Thomas Vermaelen hit a post for Arsenal.
Controversy exploded soon after, as Ireland nodded down for Wright-Phillips to instantly knock a beautifully weighted through-ball into the path of Robinho beyond Newcastle's back-line.
The dramatic turn in fortunes forced McClaren into a triple substitution, sending on Peter Crouch, Frank Lampard and Stewart Downing for Lescott, Cole and Shaun Wright-Phillips.
The pattern continued after the break, with Wright-Phillips coming close to adding a fourth after 52 minutes, turning Drogba's pass against the bar with Hirschfeld beaten.
Westermann's header from a Bastian Schweinsteiger free-kick flashed past James' post, then the Germans needed to defend well to thwart promising moves involving Wright-Phillips and then Agbonlahor.
Caca forced a good save out of Shay Given as the Danes responded but Shaun Wright-Phillips made it 2-0 with a superb strike into the top corner.
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