Archbishop Justin Welby said the Church was offering vital support in "difficult times" and said "ten times as many people" were watching online services compared to the numbers of people who were going to church in person.
The decision was made to cancel Church services last week in response to the Covid-19 outbreak, before the Government's stricter rules came into force on Monday evening that placed strict restrictions on the public and prohibited gatherings of more than two people who do not live together.
Archbishop Justin Welby told ITV News' Julie Etchingham the day they decided to close all the churches for the first time since 1208 was a "very difficult" one, but said, ultimately, it was a "very simple decision".
"We have to recognise that the church is reinventing itself with this time," he said.
"We're probably getting ten times as many people online as we had physically coming to the churches. And I think that says something about the national mood and national morale and people wanting some comfort and hope in these difficult times."
He also called on the nation to support one "another in protecting the vulnerable and in supporting our NHS" who are, he said "at their limit".
"We must not act selfishly," he warned, telling those who have been seen seemly ignoring strict government social distancing laws to "get your act together".
"If you are not complying, you are risking other people's lives, not just your own," he told Julie Etchingham.
"You are risking the health service collapsing. Do it - stick with the rules. And the sooner we do that, the sooner we can end this period of deep darkness and we can have the mother and father of all parties at the end of it to celebrate that we've got through it and we've come through as a nation United as one people.
"That's what I'm looking forward to."
The Most Revd Welby said he believed Boris Johnson had "risen to the challenge" and that anyone would "make mistakes in these circumstances".
"Nobody's perfect, but he is doing a really, really good job and he's caring about the future of this country," he said.
"We need to be a forgiving country. Understanding that there often are no simple right answers. In fact, there never are simple right answers. In this case, I watched his broadcast on Monday and I was very impressed."
Asked where God was in this natural disaster, the Archbishop said he was in "the middle of it."
"He's alongside us. He's with us, he's suffering with us. He's weeping with us."
"And when we turn to him, even in our darkest moments, we will find his presence. I know that from my own experience over long years, particularly at times such as the loss of a child or other moments of trauma and terror."
The Archbishop said he wanted to say "thank you" to all the doctors, nurses and healthcare workers.
"You are amazing. You're risking your lives, you're doing amazing work."
Justin Welby said the coronavirus crisis could offer an opportunity to heal divisions that had marked the country since Brexit.
"There is a moment of saying, we will learn from this, that ways in which we can love each other and care for each other are far greater than our divisions," he said.
"I mean, this puts the whole Brexit controversy in perspective when we're with people whose lives are risked day by day and people are coming together in the most beautiful and wonderful way supporting each other.
"If you've got a neighbour, give them a call, leave some food on the doorstep.
"Keep the social distancing care for the vulnerable. Send some money to a food bank. We are doing that. People are doing amazing things in every area. Let's keep doing that and put our differences behind us."
Coronavirus: Everything you need to know