Most Rev Justin Welby described Monday's announcement as "happy news" as he offered his prayers for Prince Harry and Meghan.
He wrote on Twitter: "Congratulations to the Duke and Duchess of Sussex on their happy news!
"Prayers for them in the months ahead."
Kensington Palace announced the pregnancy on Monday as the royal couple embarked on a 16-day tour of Australia, New Zealand, Fiji and Tonga.
Meghan, who is thought to be due in late April, has undergone a twelve-week scan. The couple tied the knot during a service at St George's Chapel, Windsor in May.
Prime Minister Theresa May tweeted: "My warmest congratulations to the Duke and Duchess of Sussex on the happy news they are expecting a baby in the Spring.
"Wishing them all the best."
Prince Harry and Meghan shared news of the pregnancy with the Queen and other members of the Royal Family during Princess Eugenie's wedding on Friday.
In a statement, Kensington Palace said: "Their Royal Highnesses The Duke and Duchess of Sussex are very pleased to announce that The Duchess of Sussex is expecting a baby in the Spring of 2019.
"Their Royal Highnesses have appreciated all of the support they have received from people around the world since their wedding in May and are delighted to be able to share this happy news with the public."
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