Dion, 42, invited 200 of the family's closest friends and family members to the ceremony at St. Elizabeth Ann Seton Catholic Church.
Eddy and Nelson wore Baby Dior baptism gowns as five godparents joined them at the alter, including their big brother R?ne-Charles, 10, Ang?lil's three oldest children, Patrick, Jean-Pierre and Anne-Marie Ang?lil, and Dion's sister Linda.
Dion's husband and manager, R?ne Ang?lil, 68, practices the Melkite Greek Catholic religion, so the ceremony included chanted prayer and traditional songs.
Dion's spokesperson said in late May that she was 14 weeks pregnant with twins, reportedly after a sixth in-vitro fertilization attempt.
Dion performed at last month's Oscars and told OnTheRedCarpet.com that she credits her post-baby figure to "breastfeeding and luck."
Dion had a reception at Caesars Palace, where Dion's new revue will open on March 15 for a three-year run.