Despite a first loss in 24 games, Guangzhou still enjoy a 12-point cushion over second-placed Beijing Guoan, who won 3-0 against Shenzhen Ruby.
Changchun took the lead after 14 minutes when Guangzhou defender Zhang Linpeng's pass was intercepted by Yovanny Arrechea and the Colombian striker steered the ball past keeper Yang Jun.
Guangzhou's best chance in the first-half came from Argentina midfielder Dario Conca but his left-footed curling effort eight minutes before the interval was denied by keeper Mi Tianhe.
Sun Xiang cancelled out Arrechea's goal 10 minutes into the second-half when he was picked out by Zheng Zhi's free-kick and headed past Mi from the close range but Guangzhou suffered a setback soon after with Chinese international midfielder Zheng receiving his second yellow card for handball.
The visitors almost grabbed a second goal 18 minutes before the end when Brazilian forward Muriqui clipped Gao Lin's pass onto the post.
Changchun, though, sealed the points when Wang Dong delivered a low cross into the path of Pei and his shot deflected off South Korean midfielder Cho Won-hee before flying into the net.
"Zheng Zhi's sending off cost us the game," said Guangzhou's Korean manager Lee Jang-soo.
"But the loss, on the other hand, eased psychological pressure on us since we felt anxious to extend the undefeated record. We'll put the defeat behind us and look forward."
Elsewhere, gals from Walter Martinez, Joel Griffiths and Xu Liang scored in the second half at Shenzhen Stadium saw Beijing Guoan overcome Shenzhen Ruby.
Meanwhile, Tianjin Teda shared the spoils with Hangzhou Greentown 2-2, while Shaanxi Baorong and Jiangsu Shuntian played out a goalless draw as did Shandong Luneng and Dalian Shide.