Packing maximum sustained winds of 140 kilometres (86 miles) an hour at the centre and gusts of up to 170 kilometres per hour, Nuri was tracked hovering over Cagayan province in northern Luzon.
"It has made landfall. She is lashing northern Luzon," said Nathaniel Cruz, chief forecaster at the state weather bureau.
"Almost all of northern Luzon is experiencing the fury of Karen," Cruz said, referring to the local name of Typhoon Nuri.
Large parts of Luzon island were drenched by heavy rain, including Manila and nearby suburbs, and schools had called off classes in some affected provinces, disaster relief officials said.
"We are prepared. We are not just looking at rain and strong winds, we are also looking at storm surges and strong waves in coastal areas," said Anthony Golez, deputy administrator of the National Disaster Coordinating Council.
Golez said provincial capitals in Luzon had been forewarned about Nuri and that contingency plans were in place.
A 72-year-old woman was killed when a landslide crushed her home near the northern city of Baguio, while a farmer was washed away by an overflowing river in the northern province of Ilocos, radio stations and local civil defence officials reported.
The general manager of the Metro Manila Development Authority, Roberto Nacianceno, said there was some minor flooding in the capital.
Rivers were also close to overflowing in provinces north of Manila, prompting the government to warn residents to take precautions. There were no reports of evacuations.
Nuri is expected to keep moving northwards and by Friday it is forecast to be just 210 kilometres northeast of Hong Kong, the government weather station said.
In Hong Kong, there were fears the storm could affect the Olympic showjumping final scheduled for Thursday evening.
The Hong Kong Observatory said Typhoon Nuri would move towards southern China, bringing wind and thunderstorms over the next couple of days, although it is not forecast to hit the city if it remains on its current course.
The Philippines is battered by an average of 20 typhoons a year, some of them devastating.
Nuri is the 12th to hit the archipelago this year.
In June, a ferry carrying more than 800 people sailed into the path of Typhoon Fengshen and sank in the central Philippines. There were only 57 survivors and many of those who perished still remain trapped inside the hull of the ferry.