Dozens of NYPD officers, on foot and driving motorcycles, escorted the remains of their slain colleague to the church.
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The solemn cry of bagpipes and drums hailed Diller's arrival at Saint Rose of Lima Roman Catholic Church in Massapequa Park, New York.
Diller, 31, was shot dead Monday during a traffic stop - the first New York City police officer killed in the line of duty in two years.
Among those speaking at Diller's funeral included his wife Stephanie, who gave emotional remarks about her husband as the "man who captured my heart, and now all of New York's."
"He wasn't the type to sugarcoat anything, so I won't sugarcoat this. This is devastating. It's a devastating and tragic loss," she said
Widow of fallen NYPD Officer Jonathan Diller speaks at funeral
On Saturday, NYPD Commissioner Edward Caban announced that Diller was promoted to Detective First Grade.
His new shield number is 110, his son's birthday.
NYC Mayor Eric Adams also spoke at the funeral, remembering Diller as a man devoted to protecting the city and its people as part of New York's Finest.
Police say Diller and his partner were investigating an illegally parked SUV when a passenger in the car, Guy Rivera, shot Diller below his ballistic vest. Diller's partner returned fire, wounding Rivera.
Adams said at the funeral that even after he had been shot, Diller fought back and disarmed Rivera.
"He ran towards danger, taking risks, making arrests and undoubtedly saving lives," Adams said.
Eric Adams delivers remarks at Officer Diller's funeral
Rivera is charged with first degree murder and other crimes, and the driver of the SUV is charged with weapons offenses. Attorneys representing the men have not responded to requests for comment.
The services Saturday follow two days of wakes this week that drew thousands of visitors, including former President Donald Trump, Gov. Kathy Hochul and Mayor Eric Adams.
During the wakes, there were emotional, tearful hugs among nurses and coworkers of Diller's wife as they rallied support around her and their 9-month-old baby boy.
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In Queens, in a moving show of support, the Mets observed a moment of silence for Diller before their home opener.
Gov. Kathy Hochul attended the wake on Friday afternoon where she spoke with the officer's family and expressed her condolences.
After that, Reps. Andrew Garbarino and Anthony D'Esposito spoke outside the funeral home and left a message for the Democratic governor.
"The governor should be focusing on fixing the issue of cashless bail in Albany," Garbarino said. "The budget was just kicked to next week. She's got a lot of power. She could fix this."
D'Esposito, a former police officer, was brought to tears when he was asked about burying his own brother in blue.
"I don't think you really ever heal. This is a terrible tragedy," D'Esposito said. "You have a 1-year-old that is never going to have a father again because we continue to allow life long criminals on the street."
Diller was on the force for three years before he was fatally shot in Queens during what should have been a routine traffic stop.
Guy Rivera, 34, was arraigned Thursday with murder of a police officer, attempted murder and criminal possession of a weapon. He remains hospitalized at Jamaica Hospital and is being held without bail.
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The other suspect arrested in Diller's death, 41-year-old Lindy Jones, was charged Wednesday with criminal possession of a weapon and possession of a defaced gun. He is also being held without bail.
Both former President Donald Trump and New York City Mayor Eric Adams attended Diller's first wake on Thursday afternoon.
Trump shared a sorrowful handshake with NYPD Commissioner Edward Caban as people waited by the masses outside the funeral home to pay their respects.
"Police are the greatest people we have, there's nothing and nobody like them and this should never happen," Trump said. "I just visited with a very beautiful wife who now doesn't have her husband."
Before the wake, Adams spoke with President Joe Biden.
"I received a call from the president a few moments ago sending his condolences and I will relay the condolences to the family, but we are truly impacted by the loss," Adams said.
A GoFundMe page for the officer's family has raised more than $500,000 and the Tunnels to Towers Foundation announced it will pay off the mortgage of Diller's home.
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