The couple tied the knot at St. Monica's Church in Santa Monica, California, back in 2009, and decided to hold 15-month-old Vivian's low-key religious ceremony at the same location this weekend.
The toddler was dressed in a white gown, which had pink lace detailing stitched across the top, while the supermodel, opting for a more vibrant attire, dressed in floral print trousers and a white blazer.
Meanwhile, the National Football League (NFL) player looked handsome in a dark navy suit and blue-and-white checked shirt, which he teamed with a black tie and matching shoes.
It is not yet known whether the pair's four-year-old son Benjamin and Tom's six-year-old son John - whom he shares with actress Bridget Moynahan - attended the baptism.
Meanwhile, the 33-year-old stunner recently admitted she was keen to have more children with Tom, 36, because she feels having kids is the most rewarding part of a marriage.
She said previously: ''I want to have a big family. My parents have been together for 36 years, and that is what I want. I've been challenged a lot by it, but it's the most rewarding part. I love kids.''
Take a look back at October's inaugural event.
The film is expected to continue without Mendes' involvement.