Takahiro Sekine fired a low opener for the hosts six minutes before the break after Nagoya's former Japan defender Marcus Tulio Tanaka failed to clear his initial header sufficiently.
Yushito Muto added a second shortly after halftime, smartly chesting home from close range after captain Yuki Abe failed to connect with a cross from the right.
Nagoya pulled one back in stoppage time with Teruki Tanaka converting after a lobbed ball caused havoc in the Urawa penalty area but the Reds held out for their fifth win of the campaign.
Mihailo Petrovic's team now have 17 points from seven matches, far happier reading than their AFC Champions League performance where they are rooted to the bottom of Group G.
Tuesday's 2-1 home loss to Suwon Bluewings was their fourth in five games, ensuring they will finish bottom of Group G.
FC Tokyo are among the chasing pack after they beat struggling Montedio Yamagata 1-0 away on Saturday.
Kosuke Ota whipped in the only goal with a left-footed inswinging free kick from the touchline in the 22nd minute which evaded everyone in the Yamagata penalty area.
They moved to 14 points, level with Kawasaki Frontale who overcame bottom side Ventforet Kofu 3-0.
Sagan Tosu are fourth on 13 points after being held to a 1-1 draw at home by Kashiwa Reysol.
Sanfrecce Hiroshima also have 13 after they beat Shimzu S-Pulse 2-0, the team greeting Kazuhiko Chiba's opening goal, the club's 1,000th, with all 11 players lying down to spell out the figure in a choreographed celebration.
Champions Gamba Osaka can close the gap on Urawa to one point with victory at home to Albirex Niiigata on Sunday.