A largely peaceful march on 20 November over the disappearances of 43 students in Guerrero state ended with riot police dispersing the crowd.
Mr Rodriquez gave no reason for his departure and the city mayor said he had stepped down immediately.
Earlier this week President Pena Nieto announced new justice and police plans.
After the 20 November protest, Mr Rodriquez Almeida said he had "congratulated his personnel for their work," in particular for "restoring public order, no matter whether others like it or not".
Lawyers for 11 people who were arrested on the day called for his resignation.
They said the protestors were arrested with no proof of criminal action and arbitrarily taken to a high security prison.
They were freed a week later due to a lack of evidence provoking accusations of abusive police practices.
Human rights groups also accused the police of indiscriminate violence during the protest against activists, journalists and bystanders.
Mr Rodriguez' departure comes after President Enrique Pena Nieto's announcement of a series of proposals to reform Mexico's security system.
Included in the plans is the replacing of local municipal police forces, which are more vulnerable to corruption, with state-level security officers.
Correspondents say Mr Rodriquez's resignation may signal a reshuffling of top police chiefs going on behind the scenes as the government attempts to plan out its new justice and policing framework for Mexico.
The 20 November protest took place during months of nationwide outrage and demonstrations against the abduction by police in the Guerrero state city of Iguala of 43 students.
State prosecutors say the municipal police were ordered by the local mayor to hand the students over to criminal gangs who executed them.
Mexico City's police chief, Jesus Rodriguez Almeida, has resigned after strong criticism of his handling of protests in the city.