So far, three deaths and 142 injuries have been reported by the Taiwan Central Emergency Operations Center after the typhoon packed winds of up to 240 kph (150 mph).
The storm hammered the eastern coast of Taiwan with torrential rain and wind for several hours prior to arrival, with photos on social media showing cars destroyed by the onslaught.
Taiwan's rugged and mountainous terrain has slowed Nepartak, which has been downgraded from a super typhoon to a typhoon by Friday lunchtime. Forecasters say the storm will leave Taiwan by late Friday and will hit eastern China early Saturday local time.
More than 16,000 people were evacuated from the worst affected areas, and an official told CNN two railway systems in the country are out of service.
Most flights are canceled throughout the morning out of Taiwan's Taoyuan International Airport.
The storm showered the region with furious winds and rain, CNN affiliate SETTV reported, and violent gusts felled trees and shattered windows in other locations.
Professional stunt rider Dave McKenna, currently in Taiwan, wrote on his Instagram account he could see roofs flying from the seventh floor of his building.
"The streets already look like a bomb has gone off, and this is just the start of it... crazy power. I've been in some back home in Australia but nothing like this," he said.
Power outages affected more than 500,000 homes, but electricity was restored to most by Friday night, the emergency operations center said.
Thousands of troops have been mobilized across Taiwan and emergency services have been ramped up, according to a Ministry of Defence spokesperson
First this year
Nepartak is Taiwan's largest super typhoon in about six years and the first for 2016 in the northern hemisphere, after an unusually quiet storm season.
Until now, the northwest Pacific had experienced its longest streak on record without a named storm
, totaling 200 days since December 2015.
On social media, meteorologists and storm chasers have been sharing their awe over the shape and size of super typhoon Nepartak, describing it as a "near-perfect" storm.
Food prices spiked in anticipation
Food prices in Taiwan jumped ahead of the storm, local media reported
, while transportation minister Ho Chen Tan promised Taoyuan International Airport would be able to withstand a direct hit from the storm.
Although the east coast of Taiwan isn't heavily populated, the rugged terrain of Taiwan enhances the risk of flooding and landslides during tropical cyclones.
Nepartak originally formed in the open waters of the Pacific on Sunday, south of Guam, and has been steadily moving to the northwest.
China braces for even worse flooding
Nepartak is expected to bring further devastating rainfall to China, which is already reeling from its worst flooding since 1998.
China Meteorological Administration issued a second orange typhoon alert Friday, the second-highest alert in the system, and recommended all outdoor gatherings be suspended and schools closed.
At least 188 people are dead or missing across 11 provinces since June 30 as a result of heavy flooding, according to the latest numbers from the country's Ministry of Civil Affairs.
Fujian, Zhejiang, Jiangsu, Jiangxi, Anhui and Shanghai are all expected to be affected by the storm.
CNN meteorologist Taylor Ward said the majority of rain would fall over southeast China, some distance from the intensely flooded areas to the west of Shanghai. He added that by the time it reached China its speed could have diminished by half to just 120 kph (75 mph).
An estimated 29 million people have already been affected by floods, hailstorms and landslides, the Ministry of Civil Affairs said, while China's Flood Control Department said the country was experiencing its worst flooding since 1998.