He is charged with murder, abuse of a corpse, tampering with evidence and related charges.
Jenna Burleigh, 22, was reported missing on Thursday night, and was last seen on security footage leaving a bar near campus in north Philadelphia, with a man police have identified as Joshua Hupperterz, 29.
A spokesperson for Lyft said the company is devastated by the allegations and stands "ready to work with the authorities in their investigation".
After speaking with Hupperterz's roommate, investigators obtained a search warrant for his apartment, just around the block from Pub Webb, Philadelphia police said.
It is not clear whether the unidentified Lyft driver knew what was in the storage bin, or where the bin was placed in his vehicle. He told them he didn't remember who he left with because he "had been so drunk".
Josh Hupperterz, a former Temple University student, was charged Sunday morning with killing Burleigh.
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Just before 9 p.m. Friday, state police officers found and arrested Hupperterz at his grandmother's home in Hawley, Pa., about 140 miles north of Philadelphia in Wayne County.
In 2013, he was charged with burglary and other offences after allegedly stealing electronics, laundry detergent and a keg of beer from a home in Scranton, Pennsylvania.
Burleigh's dad, Ed Burleigh, posted a sad message on his Facebook page on Saturday, saying: "Our Beautiful Angel Jenna is now in Heaven".
Philadelphia police Commissioner Richard Ross Jr. said Saturday the case had struck a deep chord with him as the father of a 22-year-old himself. She was majoring in film and media arts, Temple spokesman Ray Betzner said.
Last week was her first week as a Temple student after transferring from a community college.
Burleigh's body was found Saturday at Hupperterz's grandmother's property in a gated community in Paupack Twp., Wayne County.