The health-care account manager for Google was last seen about 1 pm on August 7.
Massachusetts State Police K-9 teams discovered her body in a wooded area later that night, the Boston Globe reported.
Investigators have received more than 1,300 tips from the public, but a break in the case happened after a state police trooper spotted a dark sport-utility vehicle driven by a man who matched the suspect's description, according to the district attorney's office.
The trooper wrote the license plate number on his hand and later tracked down the man's address.
The trooper went to the man's home in Worcester, Massachusetts, not far from Princeton.
There, Colon-Ortiz provided the officer with a DNA sample, the district attorney's office said.
The DNA matched a sample taken from Marcotte's hands. Police believe that Marcotte fought her attacker, scratching his face, neck and arms, the AP reported.
"It's through her determined fight and her efforts that we obtained the DNA of her killer," Early told reporters.
Colon-Ortiz is being held on a $10 million bail and will have his first court hearing on Tuesday.
Numerous local outlets - including the Boston Globe, the Telegram and Gazette and Boston's ABC affiliate - cited police sources as saying there are indications that Marcotte's body was burned.
Marcotte's Instagram feed depicted someone who loved the New England Patriots, Boston and the beach.
She died about a year and a half after she started a job at Google in New York. A Google spokesman had confirmed Marcotte's employment in an emailed statement to The Washington Post.
"Vanessa Marcotte was a much loved member of the Google team, working in our New York office for the last year and a half, and known for her ubiquitous smile, passion for volunteer work, and love of Boston sports," the statement said.
"We are deeply shocked and saddened and our thoughts are with her family and friends."
According to her LinkedIn profile, Marcotte graduated from Boston University in 2011, stayed in the Boston area for several years and worked at WordStream, an online advertising company, and Vistaprint.