The babies did not protest as Archbishop Bernard Barsi bathed their heads in water.
Prince Albert II held in his arms Gabriella who was the first twin born on Dec. 11, while his Zimbabwe-born wife Princess Charlene held Jacques throughout the ceremony in the cathedral bedecked with 6,000 white flowers.
Both babies were dressed in long baptism robes by Baby Dior.
After the ceremony, which concluded with a message from Pope Francis, the couple walked back to the nearby Prince's Palace.
Surrounded by traditional dancers they greeted friends, residents and tourists along the way, having handed the babies to their nannies.
Jacques -- who despite being the second born is the first in line to the throne under Monaco succession laws -- will on Sunday be decorated with the Grand Cross of the Order of Grimaldi.
Princess Gabriella will receive the Grand Officer of the Order of Grimaldi decoration.
For the crown prince, the godparents were chosen from Albert's side of the family, while Gabriella's godmother is Charlene's brother and her godmother, Nerine Pienaar -- wife of Francois Pienaar, former captain of the rugby team of South Africa, where Charlene spent her youth.
Albert, who was once considered one of the world's most eligible bachelors, succeeded his father Prince Rainier in 2005 at the age of 47.
He already had a daughter, Jazmin Grace, 22, after a fling with former waitress Tamara Rotolo. He denied being her father for years before DNA tests proved otherwise when she was already teenager.
The prince also has a younger son, Alexandre Coste, 11, from an affair with Nicole Coste, a Togolese former Air France hostess.
Under Monaco's inheritance laws, neither of them have any claim to royal titles or to be considered as heirs because they were born out of wedlock.
They do however have legal rights to a share of Albert's huge personal fortune, estimated by Forbes magazine to exceed $1 billion (800 million euros).
Albert married former Olympic swimmer Charlene in 2011 despite rumours that their relationship was on the verge of collapse.
Monaco — the world's second-smallest country — has 37,000 inhabitants with over 120 nationalities. Only about 8,000 who have proved their Monegasque credentials are considered Prince Albert's subjects.
Also on HuffPost