Having seen rivals Gamba Osaka held to a 1-1 draw by Vegalta Sendai on Sunday, Urawa left it late to take full advantage, but did so courtesy of 19-year-old midfielder Sekine.
Pouncing on a rebound in the Yokohama penalty area, Sekine made himself the match-winner 11 minutes from time after the hosts had been dealt an early blow with the injury-enforced removal of captain Shunsuke Nakamura.
The win leaves Urawa one victory away from sealing a first championship since 2006 as Mihailo Petrovic's side take on Gamba next week, with five points separating the top two and three games to go.
Gamba coach Kenta Hasegawa was left frustrated by a 90th-minute equaliser from Atsushi Yanagisawa at the Expo '70 Commemorative Stadium.
Kotaro Omori had given the hosts the lead shortly after the interval, but they were left contemplating a costly equaliser with Kashima Antlers and Sagan Tosu now hot on their heels for an AFC Champions League place.
Kashima came from a goal down to beat Albirex Niigata 2-1 and move third courtesy of goals from Atsutaka Nakamura and Daigo Nishi.
Tosu also came out on top by the same scoreline against Vissel Kobe after late drama at the Best Amenity Stadium - Yohei Toyoda's brace sending the home side fourth.
Kawasaki Frontale's form continues to faulter, with a fourth defeat in five J.League outings coming at the hands of Shimizu S-Pulse as the hosts went down 3-2 after twice throwing away leads.
Kazuya Murata grabbed a late winner to gain the visitors a surprise win that bolsters their hopes of survival.
Ventforet Kofu were the big winners in the battle for safety however, as they put distance between themselves and fellow strugglers Cerezo Osaka with a 3-1 win at the Yanmar Stadium.
Former Germany international Cacau gave the hosts the lead after 25 minutes but late goals from Kohei Morita, Hideomi Yamamoto and Kazunari Hosaka took Ventforet four points clear of the bottom three, while heightening Cerezo's relegation fears.
Omiya Ardija take Ventforet's place in the drop zone after a 1-1 draw with defending champions Sanfrecce Hiroshima, and already relegated Tokushima Vortis fell to a 2-0 loss against Kashiwa Reysol.
Tokyo and Nagoya Grampus played out an entertaining 2-2 draw as goals from Edu and Yoshinori Muto sent Massimo Ficcadenti's side back to the capital with a share of the spoils.
