Obama, who in 2009 became the first US president to celebrate Diwali at the White House, recalled the "wonderful time" he and his wife Michelle had celebrating the festival in Mumbai during his 2010 visit to India.
"I was proud to host the first Diwali celebration at the White House back in 2009. Since then, we've continued to mark this holiday to honour the rich traditions that define the American family," he said.
"And I know Michelle and I will never forget the wonderful time we had celebrating Diwali in Mumbai with food, dancing, and the company of friends," Obama said.
"So, to all the families gathering together this Diwali to reflect on all the blessings of the past year, I wish you a joyous celebration and Saal Mubarak," he said.
Transcript of Obama's video message:
"I want to wish a Happy Diwali to all those who are celebrating the festival of lights here in the United States and around the world.
"For Hindus, Jains, Sikhs and Buddhists, lighting the lamp-the diya -is a chance to remember, even in the midst of darkness, that light will ultimately prevail.
"Knowledge will defeat ignorance, and compassion will triumph over despair. Diwali is also a reminder that we must each do our part to achieve that victory, by dedicating ourselves to service to others.
"If we affirm our commitments to one another and strive to lift each other up, then together, we will continue moving closer to that brighter future we all seek."
Meanwhile, Secretary of State John Kerry will host the Obama Administration's annual Diwali celebration Thursday at the State Department.
In his remarks, Kerry will "celebrate the important contributions Indian and South-Asian Americans have made to the United States," a state department announcement said.
he will also "highlight the State Department's commitment to human dignity, compassion, and service - a commitment that is at the heart of all great faiths," it said.
Kerry and the Indian Ambassador to the US S. Jaishankar will then light a traditional Diwali oil lamp.