Diplomatic relations between the countries have been strained following the assassination of Kim Jong Nam, the estranged elder half-brother of North Korean leader Kim Jong Un, at Kuala Lumpur International Airport in February.
In the wake of the killing, Malaysia barred its citizens from travelling to North Korea, which prevented the national team from playing a qualifier originally scheduled for March 28in Pyongyang.
While the exact venue and time of the fixtures has not yet been fixed, North Korea's 'home' match will take place on Nov. 10 and the return tie three days later.
"We are extremely grateful for the continued support by the Football Association of Thailand in agreeing to play host for these two matches," said AFC general secretary Windsor John.
"The FA of Thailand has ensured that the AFC has been able to maintain the sporting integrity of the AFC Asian Cup qualifying."
The 2019 Asian Cup will take place in the United Arab Emirates.
(Reporting by Nick Mulvenney in Sydney, editing by Greg Stutchbury)
