The singer's flower-covered casket arrived at New Hope Baptist Church, where she used to sing as a young girl. The church is located in Houston's home state of New Jersey.
Mourners at the church, including the Rev. Jesse Jackson, fell quiet as three police officers escorted Houston's silver casket, draped with white roses and purple lilies, a couple of hours before the service.
The pop icon's daughter, Bobbi Kristina Brown, cried uncontrollably as she was comforted by Houston's close friend, Ray J.
At the end of the nearly four-hour service as her casket was lifted in the air, the weight of the moment was too much for mother Cissy Houston to bear.
She wailed, "My baby! My baby!" as she was held up by two women and led out the church behind her daughter's body.
Houston's ex-husband Bobby Brown was invited to attend the funeral, despite recent reports that he was told to stay away.
Brown arrived as the service began. He walked to the casket, touched it and walked to the back of the church. When security guards told Brown that he would be seated but the group of people he arrived with had to sit apart from him, Brown left and appeared upset.
In a statement released to the media after the service ended, Brown explained what happened.
"My children and I were invited to the funeral of my ex-wife Whitney Houston. We were seated by security and then subsequently asked to move on three separate occasions. I fail to understand why security treated my family this way and continue to ask us and no one else to move. Security then prevented me from attempting to see my daughter Bobbi-Kristina. In light of the events, I gave a kiss to the casket of my ex-wife and departed as I refused to create a scene. My children are completely distraught over the events. This was a day to honor Whitney. I doubt Whitney would have wanted this to occur. I will continue to pay my respects to my ex-wife the best way I know how."
Hours after the funeral, Brown performed with New Edition at Mohegan Sun Arena in Connecticut dressed in a white jacket, black vest, black pants and black hat.
The two were married in 1992 but divorced in 2007. Houston had sole custody of their 18-year-old daughter.
Houston died last Saturday in her hotel room at the Beverly Hilton hotel on the eve of the Grammys at the age of 48. A cause of death has yet to be determined pending toxicology reports which could take weeks.
Her death marked the end of a life that was marked by stunning career achievements and a public battle with drugs.
Both sides were recalled at the service, gospel singers BeBe Winans and the Rev. Kim Burrell joined with pop stars like Alicia Keys and Stevie Wonder in paying tribute to the pop superstar. Mourners including singer Jennifer Hudson swayed and clapped along in the aisles.
"You wait for a voice like that for a lifetime," said music mogul Clive Davis, who shepherded Houston's career for decades.
Actor Kevin Costner, her co-star in "The Bodyguard" that spawned her greatest hit, remembered a movie star who was uncertain of her own fame, who "still wondered, 'Am I good enough? Am I pretty enough? Will they like me?"'
"It was the burden that made her great and the part that caused her to stumble in the end," Costner said.
Close family friend Aretha Franklin was expected to sing at the service, but she was too ill to attend. In a statement sent after the funeral through her publicist, Franklin said she "had every intention of being there" but just couldn't make it.
"I had terrible leg spasms and locked leg muscles until 4 a.m. this morning following my concert last night, which I've been having for the last few days. I feel it necessary and very important to stay off my leg today as much as possible until concert time this evening. My heart goes out to my dear friend Cissy, Dionne, Bobbi Kristina and the rest of the family. May God keep them all."
"I didn't know her personally, but you feel like you did," said actress Chandra Wilson. "You felt like she was yours like she was a part of you and you just lost a member of your family."
Actress Vanessa Williams called Houston's death tragic and said her heart especially goes out to Bobbi Kristina.
"My heart aches for her and her family. Of course being a mother of four, and seeing what her young daughter, who was there, has to go through, it's tragic," Williams said.
To the world, Houston was the pop queen with the perfect voice, the dazzling diva with regal beauty, a troubled superstar suffering from addiction and, finally, another victim of the dark side of fame.
To her family and friends, she was just "Nippy," a nickname given to Houston when she was a child. It stuck with her through adulthood and later would become the name of one of her companies. To them, she was a sister, a friend, a daughter and a mother.
Throughout her career, she sold more than 50 million records in the United States alone. She made classics out of songs like "Saving All My Love For You," "I Will Always Love You," "The Greatest Love of All" and "I'm Every Woman." Her six Grammys were only a fraction of her many awards.
Houston has had a very public battle with drugs, which many critics blame for damaging her voice and ruining her career. Nonetheless, fans in Los Angeles say they're choosing not to remember the singer for her pitfalls, but rather her talents and her voice, which many believe was the best of all time.
"I just want to show my respect. She was a beautiful woman. She's going to be greatly missed. It's just a sad day, and I just want to come out and show my support for her and her family." said fan Tommie Rivers.
As the nearly four-hour service drew to a close, "I Will Always Love You" was played over the speaker as the casket was escorted down the aisle.
Houston is expected to be buried on Sunday beside her father in Westfield, N.J., not far from where she grew up.
We can no longer offer video clips from Whitney Houston's funeral service as the Houston family only granted permission for 24 hours.
The Associated Press contributed to this report.