A Mass for Eoghan Chada, 10, and his brother RuairÃ­, 5, was said in St Lazerian's Church, Ballinkillen, in County Carlow.
Parish priest Father Declan Foley said the boys' deaths were "beyond comprehension".
He said when their bodies were discovered, it was as "if the earth had quaked and the house had shook".
Parish priest Father Declan Foley said the pair had brought joy and happiness to their family and the community in Ballinkillen.
He reflected on the fact that last Sunday the boys had been in the church with their grandmother, helping her tidy up after Mass.
On Friday, the boys were buried in the adjoining cemetery to the church.
The service included the boy's favourite Bible story, Noah's Ark, and a reflection by Father George Augustine, an Indian priest from Portlaoise.
"Their deaths have stunned the whole community but particularly the parents of their classmates, and their big concern was how they were going to tell their own children this sad news," Fr Foley said.
On Friday, a judge ordered that the boys' father, who is charged with their murder, should undergo medical treatment.
Sanjeev Chada, 43, from Ballinkillen, County Carlow, was further remanded in custody when he appeared before a district court in County Roscommon.
The bodies of Eoghan and RuairÃ­ Chada were discovered in a vehicle driven by their father in County Mayo on Monday.
Their father was charged with their murders on Thursday night.

The 24-year-old from Runcorn became Britain's first champion in the event's 17-year history in 2016.
After winning gold in the season-opener in Switzerland earlier in April, she finished behind 18-year-old Janja Garnbret in Chongqing, China.
Coxsey still leads Slovenia's Garnbret in the overall rankings, with five more events to take place before August.
Japan's Akiyo Noguchi, 27, picked up bronze with third place.
"It was a hot and sweaty final," Coxsey wrote on Twitter. "I'm very happy to finish in second place. Massive congrats to Janja!"
Sport climbing - which includes bouldering - is one of five new sports confirmed for the 2020 Tokyo Olympics.
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WATCH: How Shauna Coxsey became the UK's first bouldering world champion

The 35-year-old ex-England batsman, who made his highest Twenty20 score with 115 not out from 66 balls on Wednesday, hit seven sixes in 100 from 45 balls.
It took Durban-based Dolphins to their 168 target as they beat the Knights by nine wickets with 20 balls to spare.
Pietersen will appear in two more games for the Dolphins before heading to Australia for the Big Bash League.
The South Africa-born batsman last played for England in the 2013-14 Ashes whitewash in Australia and was told in March that year that he was not part of England's future plans.
Meanwhile, there was a new Twenty20 world record in New Zealand as former Kiwi opening batsman Peter Fulton claimed five outfield catches for his Canterbury province against Northern Districts in their domestic Super Smash T20 league.
Listen to BBC World Service's Stumped programme, featuring an interview with Kevin Pietersen.
Hundreds of people have attended the funeral of two young boys found dead in the boot of a car in County Mayo.
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Shauna Coxsey took silver in the second Bouldering World Cup event of the year as she continued her title defence.
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Kevin Pietersen smashed a second successive unbeaten hundred in South Africa's Ram Slam T20 event.