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Ahmad Khan Rahami was also charged with various weapons possession counts, Union County Prosecutor Grace H. Park said.
The FBI and NYPD were expected to file charges of their own, along with authorities in Ocean County.
The 28-year-old Elizabeth resident -- a native of Afghanistan who was graduated from Edision High School -- was wanted for questioning in connection with Saturday night's bombings in midtown Manhattan and Seaside Park, as well as several bombs found at a train station near his home.
A bar owner in Lindon found him sleeping in the tavern doorway Monday morning and called police from another business he owns across the street after recognizing Rahami, authorities said.
A shootout followed in which Linden Police Officers Angel Padilla, Peter Hammer were injured, authorities said.
Rahami emigrated to the U.S. in 1995 as a child after his father came seeking asylum, authorities said. He graduated high school in 2007 (see photo, above) and became a naturalized citizen four years later, they said.
Investigators believe Rahami acted alone, FBI Assistant Director William Sweeney said during a Manhattan news conference.
Officials with the FBI's Newark Field Office say they "would like to thank all the hard working men & women of law enforcement who have worked around the clock to apprehend Rahami."
The bureau also honored "the heroism of the Linden PD. Wishing a fast recovery to the 2 wounded officers."
Linden police got a call about 10:30 a.m. of a man sleeping in the doorway of a local bar, which was closed, Linden Police Capt. James Sarnicki told MSNBC .
A responding officer found Rahami, he said.
"Show your hands," the officer told Rahami, the captain said.
Rahami pulled a gun and fired one shot, hitting the officer in the abdomen, he said. The officer's bulletproof vest took most of the blow.
The officer returned fire and Rahami walked down the street, "indiscrimnately firing his weapon at passing vehicles," Sanicki said.
Several officers responded -- one of whom was hit in the face with shrapnel, he said.
Rahami was shot several times but was conscious when loaded into an ambulance, authorities said.
Authorities said they also secured a backpack that Rahmani was carrying and were awaiting a bomb squad and K9 unit in the 500 block of Elizabeth Avenue in the Union County town.
Rahami is a naturalized U.S. citizen born in Afghanistan, said authorities who also conducted several raids Monday morning Elizabeth, where five bombs were found in a train station.
They also took five people into custody Sunday night after stopping a "vehicle of interest" on the Belt Parkway just coming off the Verrazzano Bridge, NY state Sen. Marty Golden reported.
The first weekend explosion was in a trash can near the Seaside Park boardwalk as a charity 5K race to benefit U.S. military members was about to begin Saturday morning. No one was injured and the race was cancelled.
Then came another trash can bombing at 23rd Street off Seventh Avenue that injured 29 people around 8:30 p.m. Another device was found blocks away.
Several “improvised explosive devices” were found packaged Sunday night in a trash can near the Elizabeth train station, the FBI said. It denoated while a robot was securing it, but no one was injured, the bureau said.
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