The number of people injured was 10 times more than reported Wednesday, the Xinhua news agency said, citing the latest official tally.
The 38 dead were recorded in Guangdong province, including 20 in Shenzhen city, nine in Huizhou city, two in the capital Guangzhou, one in Shantou city, three in Shanwei city and three in Dongguan city, the Southern Daily's website said.
The typhoon, considered the worst to hit Guangdong's Pearl River Delta since 1979, pummelled the province Tuesday evening and stayed in the area for 13 hours, leaving a trail of destruction.
Many of the deaths happened due to the collapse of poorly built structures, especially shacks used to house migrant workers.
Shenzhen -- an economic boom town bordering Hong Kong and the first city in China to be declared a special economic zone in the early 1990s -- suffered the most damage.
More than 2,000 temporary structures, such as shanties, were toppled.
The city draws a large number of migrant workers from all over China but many of them are not properly housed and live in shacks, especially on construction sites.
Most of Shenzhen's deaths occurred at a construction site where a factory was being built with 16 migrant workers killed when the partly built two-story factory collapsed onto the shanties they were living in.
Shenzhen is teeming with construction sites as there is a strong demand for factories from investors who use the city as a cheap production base.
Apartment buildings are also going up quickly to satisfy neighboring Hong Kongers' increasing desire to buy homes across the border.
The Shenzhennews website cited statistics showing more than 80 percent of the deaths from typhoons in Shenzhen in the past 20 years resulted from the collapse of "simple houses".
Based on preliminary estimates, the impact of Typhoon Dujuan on Shenzhen was greater than previous typhoons in the past two decades, according to Shenzhennews.
In addition to the 20 killed in Shenzhen, 20 others suffered serious injuries, while 78 suffered light injuries and two people were missing.
Shenzhen's vice mayor Liang Daoxing had called a meeting before the typhoon to remind local officials to take precautionary measures, including inspecting dangerous structures and relocating residents from unsafe buildings.
But anti-typhoon measures were not properly carried out and out-of-town residents were not informed how to protect themselves in the event of a typhoon, leading to the high number of casualties, Shenzhennews said.
A Guangdong spokesman said province-wide economic losses reached around two billion yuan (241 million US dollars), according to Xinhua.
Highways, telecommunications infrastructure, water and power supplies, irrigation systems and crops suffered serious damage.
In Huizhou city alone the typhoon destroyed 12,000 hectares (29,000 acres) of cropland and 13,785 houses and facilities, Xinhua said.
Authorities in Guangdong have relocated 92,718 people living in dangerous structures to more secure buildings to prevent further casualties, the Southern Daily said.
Coast guards had also rescued 23 stranded fishermen.
Dujuan, which had wind speeds of more than 40 meters per second, weakened to a tropical storm that faded into neighboring Guangxi province Wednesday.
By Thursday, schools had reopened and transportation services, including flights and trains had resumed normal operation.