Sanfrecce - the defending champions - were one of four sides to have already resumed the J-League season after a two-month break for the World Cup, while the 14 other sides all restarted on Saturday.
It has been an indifferent campaign for Sanfrecce, but they appeared well on course for all three points at the NACK5 Stadium.
Hisato Sato's double and Naoki Ishihara's fifth league goal of the season had put Sanfrecce 3-0 ahead by the 26th minute.
Hajime Moriyasu's men could not have expected what followed considering that Omiya are in 17th position and have won just three games this season.
Rock-bottom Tokushima Vortis grabbed a rare point in a 1-1 draw at relegation threatened Nagoya Grampus, while Cerezo Osaka earned a 2-2 draw with Yokohama F Marinos thanks to Kenyu Sugimoto's injury-time leveller.
Sagan Tosu remain just a point adrift in second as Kim Min-woo's goal secured a 1-0 triumph at Vissel Kobe, while Kawasaki Frontale - who occupy the final AFC Champions League spot - were 2-0 victors on their visit to Shimizu S-Pulse.
Ten-man Kashima Antlers retain hopes of continental football next season, but could only draw 1-1 at Tokyo in the capital, while Kashiwa Reysol and Vegalta Sendai played out a 0-0 draw.
