The suspect, identified as Chandrabhan Sanap (38), has been apprehended from Nashik and placed under arrest after being brought here, police said.
Sanap was produced before a local court which remanded him in police custody till March 15, police said.
Sanap resembled the man who was spotted with Esther in a CCTV footage at the Kurla railway terminus on January 5, the day she went missing, they said.
The victim's decomposed body was found off the Eastern Express Highway in suburban Bhandup on January 16.
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"During the probe, SIT has picked up the suspect from Nashik (which is about 171 kms from Mumbai)," police said.
The 23-year-old victim, a native of Machilipatnam in Andhra Pradesh, was employed with IT major TCS at its office in suburban Goregaon.
Police recently released the photograph of the man who was spotted with her in the CCTV footage at the station. The man was carrying Esther's luggage.