Francisco Salgado Valladares, who was deputy director of the southern city of Iguala's municipal force, was detained by federal police officers, two Mexican security officials said on condition of anonymity.
Local media said Salgado, who was one of the most wanted fugitives in the case, was captured in Cuernavaca, a picturesque weekend getaway for Mexico City residents just 90 kilometers (50 miles) south of the capital.
Prosecutors say Iguala's gang-linked mayor ordered police to intercept the students on September 26 over fears that the aspiring teachers, known for their regular protests, were in town to disrupt a speech by his wife, AFP reported.
The officers rounded up 43 students and handed them over to the Guerreros Unidos drug gang, which slaughtered the young men and incinerated their bodies, according to prosecutors.
Some 100 people have been detained in the case, including several municipal officers, gang suspects, and Iguala's mayor Jose Luis Abarca and his wife.
The city's top security official, Felipe Flores Velazquez, remains on the lam in a case that has sparked protests against President Enrique Pena Nieto's administration.