Alberto Zaccheroni's side proved far too good for Azerbaijan with the Borussia Dortmund man netting, while Ryo Miyaichi made his international debut
The Samurai Blue were using the game against the 109th-ranked Azerbaijan as preparation for their upcoming final round 2014 World Cup qualifiers against Oman, Australia and Jordan, although the friendly never hit any great heights.
Kagawa's strike and an Agil Nabiyev own goal settled the contest, while Arsenal's Ryo Miyaichi made his international debut off the bench in one of the game's rare highlights.
Earlier, Shinji Okazaki had the first real opening when Inter full-back Yuto Nagatomo whipped in a low cross, but the Stuttgart man couldn't convert.
On 17 minutes, the hosts had the ball in the back of the net when Makoto Hasebe's shot fell to Takayuki Morimoto, who lashed it home only to be ruled marginally offside. The Novara man would limp off with an ankle problem before the interval putting in doubt his involvement in the upcoming qualifiers.
Barely a minute later, Kagawa dragged a shot wide from the edge of the box, while Keisuke Honda saw a 35-metre free-kick hit the post after an unconvincing save from Kamran Agayev.
Japan upped the ante shortly before the break and eventually the breakthrough came on a swift counter-attack as Honda produced a neat flick for Hasebe to run onto and his well-placed ball found Kagawa, who beat a defender inside the box before a calm curling finish for 1-0.
Ufuk Budak then forced a good save from Japan keeper Eiji Kawashima as the hosts headed into the interval with a narrow advantage.
The Samurai Blue started the second 45 slowly, with Azerbaijan striker Cihan Okzara forcing his way forward before shooting into the side netting.
However on 58 minutes Japan had a second, when Kagawa whipped in a cross which Honda headed goalwards, only for Okazaki to scramble it home from close range with the aid of a deflection off Nabiyev.
Miyaichi replaced Kagawa past the hour mark, with the Arsenal man's introduced greeted by the Shizuoka crowd. The teenager curled a shot which was saved by Agayev on 72 minutes, while his high ball from the left flank found Okazaki but he couldn't keep his header down.
Azerbaijan almost pulled a goal back on 82 minutes when a free-kick drifted past a crowd of players, falling to defender Nabiyev but he could only manage a slight touch before it hit the post.
Substitute Kengo Nakamura had a late chance but was denied by Agayev as Japan settled for a routine victory over their East European opponents.
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