Japan took to the field without their European-based players, including Celtic star Shunsuke Nakamura, first-choice goalkeeper Seigo Narazaki and key centre back Yuji Nakazawa.
Both Narazaki and Nakazawa will also miss the 19 November qualifier in Doha through injuries.
The scoring was opened just three minutes into the action when FC Tokyo left back Yuto Nagatomo dribbled down on the break, stepping aside the Syrian defence and slotted the ball past goalkeeper Mosab Balhous.
Nagoya striker Keiji Tamada put Japan 2-0 up on 26 minutes when his left-foot volley ruffled the net on a right cross from Kengo Nakamura.
In the 62nd minute, Vissel Kobe frontman Yoshito Okubo pleased the crowd at his home stadium by hitting the back of the net on a deflection off Syrian defender Adelkader Dakka.
Syria, who narrowly missed the final Asian qualifying round, pulled one back on a penalty from Mohamed Al Zeno in the 78th minute when Shinji Kagawa pulled down Mahmoud Al Amenah in the box.
"It was great that my players kept their motivation high," Japan's under-fire coach Takeshi Okada said. "The team tried almost everything I wanted to test."
"But we must not forget that this result won't guarantee us anything for the Qatar match," he said.
Okada, whose second stint as national coach began when he took over from Ivica Osim when the Bosnian suffered a stroke a year ago, has come under pressure after a recent run of uninspiring results.
Japan, who beat Bahrain 3-2 away in their opening qualifier, were held 1-1 by Group 1 underdogs Uzbekistan at home on 15 October, a week after a 1-1 friendly draw with the United Arab Emirates.
Japan are level with Qatar on four points, trailing Australia, who have a maximum six points from two games. Bahrain and Uzbekistan have one point each.