Reuven Simon and Joseph Sebastian died after getting into difficulty at Enagh Lough on Monday evening.
The joint Requiem Mass was held at St Mary’s Church in Ardmore.
Pupils from St Columb’s College in Derry, which the boys attended, formed a guard of honour outside the church on Friday morning.
The mass was conducted according to the rites of the Syro-Malabar Church.
The Reverend Father Clement Padathiparambil, head of the church in Ireland and the chief celebrant of the funeral mass, told mourners that Reuvan and Joseph, who were from Derry’s Indian Keralan community, were “special in so many ways”.
Hundreds of mourners filled St Mary’s while many more gathered outside the church to watch the service on a big screen.
During his homily, parish priest Father Michael Canny said the boys had been taken from their families “suddenly and tragically”.
“In the eyes of this world you, their families and this community, have lost two young boys at a beautiful time in their lives when they were filled with hopes and dreams,” he said.
Both boys, he said, were passionate about football and cricket and had “flourished in their education”.
Their “kind and gentle natures won them much affection among staff and pupils alike”, he said.
Speaking on behalf of the Sebastian family, Abraham Sebastian said Joseph was a “wonderful and sweet child”.
He had grown to be “a strong and steadfast teenager, a young man with so many plans for the future”, Mr Sebastian said.
Both families were in the midst of an unimaginable tragedy, he said.
Reuven’s cousin Juliet told the service he was among the sweetest and kindest people she had ever known.
He spread positivity and would “light up every room,” she said, and always wanted to make his family proud.
Reuven, she added, “lives on in everyone’s hearts”.
Bishop of Derry Donal McKeown said Reuven and Joseph were “a huge gift to all of us in their life”.
He added: “I know that the Syro-Malabar Church community is very strong and close-knit.
“They will work together to support the bereaved and the traumatised through the next difficult weeks and months”.
The boys were pupils at St Columb’s College and had received their GCSE results last week.
They were part of a group who decided to go for a swim while out cycling on Monday.
Deacon at St Mary’s Church, Shaun Doherty, said the tragedy had devastated the community.
“This type of loss is so rare and so painful that our hearts just go out to the family, friends and the wider community who are suffering at this terrible time,” he said.Finbar Madden, principal of St Columb’s College, said the boy’s deaths were “so so hard” for students and teachers to comprehend.
“Two fabulous young boys who today was meant to be their first day back at the school, starting year 13 but instead we are gathered here in Ardmore for their funeral.”
“I think you can see from the number of St Columb’s boys that turned out what these two young men meant to the school.
“These two boys were very special, they were friends in life and very much friends in death.”
A book of condolence was opened to the public at the Guildhall in the city by Mayor Sandra Duffy on Wednesday afternoon and can also be signed online.
Following the Requiem Mass, the remains of Reuven and Joseph were interred in the cemetery adjoining St Mary’s Church.
A candlelit vigil was held on Thursday night at St Oliver Plunkett’s Church in Strathfoyle to pay tribute to the two boys, whose wake was held in St Columb’s Church in the Waterside.
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