Second-half substitute Cole scored twice to spare England’s blushes.
But he suffered a blast from the angry England boss who had become increasingly frustrated at the way his side were playing.
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Capello rose from the dug-out, strode towards the touchline and exchanged angry words with Cole and Rooney.
The manager admitted: “Did I have a row with them? Yes.
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“I was upset that they had both dropped far too deep into the midfield which meant Emile Heskey was then left alone up front.
“I made my feelings plain to them that they needed to get further forward and offer Heskey more support. That’s what I said to them.”

And match-winner Cole confessed: “Our confidence was a bit low but this is a small step on the way to qualifying. I was told to go on and make something happen.
“It needed a spark and we got the job done in the end.
“Andorra made it difficult for us, we had a lot to prove but people should judge us after Wednesday’s game against Croatia.”
Capello, though, denied he had laid into the side at half-time despite what turned out to be an increasingly poor and goalless first half.
He insisted: “No, I did not lose my temper with them during the half-time break. All I did was explain to them they needed to raise the tempo.
“I made the changes to bring on Heskey because of his pace and movement and also bring on Joe Cole to offer us something different on the left.
“The only reason I sent the players back out on to the pitch early after the break was that it was far too hot in the dressing room.”

But no doubt Capello will have made his feelings known in stern if not vexed terms during the break.
As the first half wore on the new coach looked continually agitated as he leapt from his seat, made angry gestures and muttered under his breath.
He explained: “We started very well and Theo Walcott in particular was incredible in the first 15 or 20 minutes.
“He showed so much pace and helped create at least three chances which we should have taken.
“But after that early good start we started to slow down and made the wrong sort of passes. But, that said, it was not easy when they always had nine men just in front of the penalty box.”
It took the sharp movement and classy finishing of two-goal Cole to turn half-time boos from the England travelling fans to relieved applause by the final whistle.
Capello added: “It has been a good time lately for Joe Cole. He scored the late equaliser in our last game, the 2-2 draw against the Czech Republic, and now he has scored another two.

“I haven’t decided my starting 11 in Croatia but obviously he is now a player very much in my plans.”
But he warned: “Of course it’s going to be a very different game in Zagreb.”
Cole is determined to play in midweek to bury the heartbreak of missing out on Euro 2008.
He admitted: “At first I couldn’t watch anything during the Euros. But I’m a fan like everyone else so I tuned into it in the end. I was very impressed with what I saw of the Croatians.
“It was heartbreaking every day to turn on the television but you just have to deal with that as best you can and put it right next time.”
The Chelsea midfielder scored within four minutes of his introduction as substitute for the ineffective Stewart Downing last night.
And he added: “When you come on you just want to make an early impact. Two chances came my way and I took them.
“I understand the manager and he has his reasons not to pick me — but the main thing now is Wednesday.
“I’ve had a decent start to the season and now I want to keep it going and keep hitting the back of the net.
“It was a big win for us because every three points is big, whether it’s Croatia or Andorra.
“It was a frustrating dressing room at half-time but they made it frustrating. There are no excuses and we don’t need any because we won in the end, but there were some nerves and cobwebs out there as it has been a long time since our last qualifier.
“I have to say I thought the fans were great. We know we haven’t given them enough to shout about recently but, whatever people think of footballers now, we do care and want to get to South Africa for them.
“Hopefully now we can move on.”

Cole’s touch in front of goal is in stark contrast to Rooney — who has not found the net since October 2007 against Russia.
But the Manchester United star insists he is not suffering a confidence crisis as his international goal drought continues.
Rooney blasted high and wide early in the first half after Walcott’s clever touch created an opening.
And he admitted: “I thought I should have done better with the chance I had and that’s why I showed a bit of frustration.
“But I’ve only played two games for my club and two games for my country this season, so I wouldn’t call it a crisis.
“These games are always difficult. I’ve experienced it before with United but maybe not a side playing so deep. Yet, thankfully, we got the goals we deserved in the end.
“It can be frustrating when they just kick the ball forward and defend. It’s weird but we were patient.
“I wasn’t too concerned because it was similar to the last time we played them. They wanted to upset us.
“The win has given us confidence going to Croatia. We know what they did to us in the Euros and all the players want to put that right.
“We were expected to get the three points here but Croatia will be much more competitive.
“It’s a chance to put the record straight but we know they are a good team.”
Rooney tried to play down his bust-up with Capello.
He said: “The manager wanted to give us some tactical advice because of how tough they were to break down, so he was just telling us a few different things.”