The visitors went into the game on the back of an impressive 2-0 victory over Kashiwa Reysol but Yuji Okuma's men were unable to build on last weekend's win as they went down to goals in either half.
Hiroyuki Abe opened the scoring with his seventh league goal of the campaign prior to the interval before Akihiro Sato put the game out of Cerezo's reach a minute from time.
It denied the visitors the chance to edge clear of the bottom three while Gamba's third consecutive league victory keeps them in the race for an AFC Champions League place.
A point in the derby would have proven enough to move Cerezo out of danger after Ventforet Kofu were beaten 2-0 by Nagoya Grampus in the day's other early kick-off.
Asahi Yada and Kensuke Nagai were on target as the hosts extended their unbeaten run in the top flight to five matches.
Fellow strugglers Shimizu S-Pulse lost 3-1 at Vissel Kobe, and Vegalta Sendai were beaten 2-1 by Sagan Tosu, while second-bottom Omiya Ardija sent rock-bottom Tokushima Vortis closer to the drop with a 2-0 win at the Pocari Sweat Stadium.
Tokushima sit 10 points adrift at the bottom after Dragan Mrda struck for the visitors, who appear to be finding some form and have moved to within two points of safety.
In the battle for the title, Urawa Reds took another step towards their first J-League crown since 2006 with a 3-1 win against 10-man Kashiwa Reysol.
Daisuke Nasu, Yosuke Kashiwagi and Shinzo Koroki were the men on target for the leaders as Kenta Kano was dismissed for the visitors early in the second half.
With Kawasaki Frontale held to a goalless draw by Tokyo, Urawa lead the division by six points while Kashima Antlers bounced back from their shock defeat Omiya.
Yasushi Endo's goal proved decisive as Kashima saw off Yokohama F Marinos to stay within reach of an AFC Champions League places.
Elsewhere, Sanfrecce Hiroshima defeated Albirex Niigata 2-0.
