Bieber flew unannounced to the central city of Tacloban just over a month after it was devastated by Super Typhoon Haiyan and sang Christmas carols to children at a heavily damaged local school amid tight security.
"He sang 'Holy Night' for the children," said Kate Donovan, a spokeswoman for the United Nations Children's Fund (UNICEF), one of three aid agencies expected to benefit from Bieber's charity work.
During the performance, a boy hopped on the improvised stage and danced to the 19-year-old Canadian superstar's lead, an AFP reporter saw.
"Most touching trip of my life," the singer said on Twitter, also describing the performance as the last stop and "the most important one" of his global "Believe" tour.
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"I saw the devastation first hand today. They need our help," he added.
Prior to visiting the Philippines, Bieber had posted a message on fund raising website Prizeo.Com urging his millions of fans to donate to the victims of the typhoon, the strongest to ever hit land.
"Justin brought a lot of joy, hope and cheer to the hundreds of children who were there," she added.
The money that would be raised would give child survivors access to education, vaccinations, clean water and sanitation, she said.
Haiyan cut across the central Philippines on November 8, destroying scores of communities along its path.
Tsunami-like storm surges it triggered also swallowed up many coastal areas, and were blamed for majority of the nearly 6,000 deaths.
In his message on Prizeo, Bieber, one of the most followed persons on Twitter and best known for hit songs such as "Baby," "Boyfriend" and "Beauty and a Beat", said those donating to his cause could win a chance to personally see him record music next year.
"In the wake of Typhoon Haiyan, its victims in the Philippines need our help -- and they need it now," the singer said in his appeal.
Many other international celebrities have also lent their voices to the massive rehabilitation effort, including Grammy-award winning singer Alicia Keys who visited victims airlifted to Manila two weeks ago.