The monarch was due to return to London on Monday ahead of a busy schedule of events including a meeting with U.S. President Donald Trump on Friday at her Windsor Castle home.
The Archbishop of Canterbury Justin Welby welcomed the royals at the entrance to the chapel.
Kensington Palace announced earlier today that Louis will have six godparents, including some of William's oldest friends business developer Nicholas van Cutsem, businessman Guy Pelly and Harry Aubrey Fletcher, alongside Lady Laura Meade, and Kate's school friend Hannah Gillingham and her cousin Lucy Middleton.
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Later as she left the ceremony, the confident young Royal showed off her sunny nature as she gave a cheery wave to crowds gathered outside the chapel at St James' Palace, carrying the large Order of Service under her arm.
After the 40-minute ceremony, the families went to Clarence House for a tea party where guests were to be served slices of the traditional christening treat, a tier taken from Will and Kate's 2011 wedding cake.
It's days like today that make being a mom so special for Kate Middleton.
Charlotte, who is three, was christened in 2015 at the 16th-century Church of St Mary Magdalene on the queen's country estate in Sandringham in eastern England.
The chapel is where Queen Victoria married Prince Albert in 1840. In April he underwent planned hip surgery, but attended the wedding of Prince Harry and Meghan Markle just a few weeks later, walking unaided.
This is not the first time the royal family has commented on the baby prince's knack for snoozing.
The Prince has promised to build an exclusive library for Louis in memory of Princess Diana and the 1926 AA Milne classic is the library's first book.