Bobby Brown was seen to walk to her flower-covered coffin at the front of New Hope Baptist Church in Newark, New Jersey, and touch it before walking out.
Their tumultuous 15-year marriage came to an end in 2007 following allegations of domestic abuse and her much-publicised battle with drug addiction.
Gospel choirs filled the church, where Houston herself performed as a child, with song while Alicia Keys, who described her as an "angel" and a "beautiful human being", also performed.
Meanwhile actor Kevin Costner, who starred with Houston in The Bodyguard, described her during the service as the "greatest pop star in the world".
Houston, 48, was found submerged in the bath in her hotel room on the fourth floor of the Beverly Hilton in Los Angeles last Saturday.
The death of the star, one of the world's best-selling artists in the 1980s and 1990s, prompted a worldwide outpouring of grief, but her family decided that they wanted her funeral to be a private invitation-only event.
Stevie Wonder also performed, describing it as "such an emotional moment".
"I had so much respect for her love for music," he said as he sat before a grand piano at the front of the church.
Aretha Franklin was also meant to sing but was said to be too ill to attend.
Despite the hundreds of mourners present, the Baptist service retained an intimate feel, with many personal tales of Houston recited to laughs and applause from the congregation.
Describing working with her on the 1992 film, Costner said Houston was "as beautiful as a woman could be".
He went on: "The people didn't just like you Whitney, they loved you.
"You're gone too soon, leaving us with memories of a little girl who stepped in front of this church, in front of the ones that loved you first, in front of the ones that loved you best, and loved you the longest.
"Then boldly you stepped into the white hot light of the world stage and what you did is the rarest of achievements, you set the bar so high."
Pastor Joe A Carter led prayers and told mourners: "Whitney, you are the only one that can bring all of us together. Whitney, today is your day. We celebrate."
Newark Mayor Cory Booker told the congregation: "We are here to mourn our loss but to celebrate her life. We love you Whitney."
R'n'B singer R Kelly sang Houston's own hit I Look to You as her daughter Bobbi Kristina Brown and mother Cissy Houston looked on.
Other prominent gospel singers including Andrew McClurkin, Kim Burrell and brother and sister Bebe and Cece Winans also gave performances, with Bebe Winans joking that he would most miss "crazy Whitney".
Actor and director Tyler Perry said Houston's "grace led her to the top of the charts".
"There was a grace that kept on carrying her," he added.
Houston's cousin, soul singer Dionne Warwick, read a poem, while her long-time mentor, music mogul Clive Davis, and her sister-in-law Patricia Houston also spoke during the lengthy service, which lasted three hours and 45 minutes.
Houston's most famous song I Will Always Love You was played over speakers in the church as the coffin was carried out and guests began to leave.
Thousands of fans of the singer were also gathered outside the church to pay their last respects.
Houston's final resting place will be next to her father John at the Fairview Cemetery in Westfield, New Jersey. He was buried there in 2003.
At the peak of her success Houston won multiple Grammys including album and record of the year, and sold millions of albums and singles worldwide.
But her career began to unravel as she battled with drug addiction, spending various spells in rehab. Her voice also began to suffer, prompting record sales to nosedive.
Houston appeared on the X Factor in Britain in 2009 and released a new album after seven years off the scene.
The cause of her death remains unclear and the results of toxicology tests are awaited.
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