SIPG were seconds away from moving into a three-way tie, level on 16 points, at the top of the standings with Guangzhou Evergrande and Guangzhou R&G but Ding's goal scuppered those hopes.
He Guan gave the Shanghai side the lead in the 52nd minute, only for Ding to level from close range four minutes into injury time to secure Chongqing a share of the points.
"This result was not what we were expecting," said Villas-Boas, whose team advanced to the knockout phase of the Asian Champions league during the week. "They equalised at the last moment.
"We had a pretty good performance over the 90 minutes and a draw was not consistent with that. We missed some good opportunities. We could have led by two goals and we were the better side in the second half."
Guangzhou Evergrande topped the standings on Saturday after a Ricardo Goulart hat-trick, which included two penalties, saw Luiz Felipe Scolari's side claim a 4-2 win over Henan Jianye 24 hours after Guangzhou R&F suffered a surprise 3-1 defeat against Guizhou Zhicheng.
Those results mean the pair are level on 16 points from the first seven games of the campaign, with Evergrande ahead with a better goal difference.
"I can't say that we are increasing the level of our performance," said Scolari, despite seeing his team win their fourth game in a row in all competitions.
"You could see that in the first four rounds our opponents were strong sides such as Shanghai SIPG, Shandong and R&F. They were all tough games, and now our results are also within my expectation."
SIPG are in third, two points further behind, while Shandong Luneng remain in fourth after their meeting with Shanghai Shenhua was postponed due to repair work being conducted at Shenhua's fire-damaged Hongkou Stadium.
Ezequiel Lavezzi scored twice as Manuel Pellegrini's Hebei CFFC handed Tianjin Teda a 4-0 thrashing to move up to fifth place while Beijing Guoan had two-goal Renato Augusto to thank as they notched up their first win in three games with a 4-2 victory over Liaoning Whowin.
Yanbian Funde picked up their first win of the season with a 1-0 victory over Changchun Yatai while Jiangsu Suning's struggles continued with a third draw of the season, this time a 2-2 tie with Tianjin Quanjian, leaving Choi Yong-soo's team rooted to the bottom of the standings.
(Reporting by Michael Church in Hong Kong, Editing by Pritha Sarkar)
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