"It's the least we could do," said Tour director Christian Prudhomme.
"Eddy Merckx is an exceptional champion and a person of exceptional humility."
"I'm very emotional, I hope I'll still be alive!" said the 71-year-old Merckx, a three-time world champion who holds the record for the most stage wins on the race, and who also won the Giro d'Italia five times and the Vuelta a Espana once.
Paris mayor Anne Hidalgo added the 2019 Tour "will link Brussels to Paris, two cities that have recently suffered greatly from terrorism".
"We wanted to find an event that ties our two cities."
Brussels has hosted the Grand Depart once before, in 1958. It will be the 23rd time a country outside France has been chosen for the start of cycling's most famous stage race and the fifth time from Belgium.