The victory, which came after the hosts scored twice in the last 16 minutes to overhaul Tajikistan, also ensured group rivals Yemen would qualify for Asia's continental championship for the first time.
The pair join fellow new boys Kyrgyzstan in the draw on May 4 for next January's tournament in the United Arab Emirates.
Younghusband, who scored a 90th minute penalty to give his side the win in Manila, said he hoped Philippine football was now on the rise.
"Hopefully this is the catalyst for more growth in Philippine football," he said.
"In 2010, we got a lot of support from the private industry and hopefully this moment can spur a resurgence in Philippine football, get people to talk about Philippine football again."
Football in the Philippines, and in other nations that have sat outside Asia's established elite, is likely to receive a significant profile boost thanks to the 2015 decision to expand the quadrennial finals from 16 to 24 nations.
Throughout the last two decades, football in Asia has been dominated by the same small group of nations, who have monopolised the continent's World Cup berths and Asian Cup success.
Japan have won the title four times since 1992, Saudi Arabia, South Korea and Iran are often among the contenders, while Australia joined the confederation in 2006 and won the most recent edition on home soil three years ago.
Increasing the number of teams at the finals is unlikely to end the dominance of those nations any time soon, but opening up more places should provide improved opportunities for other countries to break into the Asian elite.
Yemen booked their place at the tournament despite not being able to play in front of their own fans due to the ongoing security issues at home, while Kyrgyzstan sealed their berth last week.
Vietnam, building on their run to the final of the Asian U23 championship in January, will be returning to the finals after missing out in 2011 and 2015, while India return will be making only their second appearance in 35 years.
In addition to Kyrgyzstan, former Soviet republics Uzbekistan and Turkmenistan have also qualified.
(Editing by Peter Rutherford)
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