The 2007 IRB Player of the Year became the sixth person in test history to reach the milestone, managing it in his 86th appearance for the Springboks and helping the side to a 56-23 victory.
"It is a wonderful effort, to score 50 tries in a career at all levels of rugby is great, but to score 50 for your country in tests is outstanding," De Villiers told reporters.
"He is a classy player, but has also put in a lot of hard work over the years. There always seems to be magic when he touches the ball. Hopefully there will be many more."
Habana will join French side Toulon at the end of the Super Rugby season, one of a number of Springboks who are looking to cash in on lucrative deals in Europe and Japan.
But unlike most who are forced to give up their international careers when moving away from South Africa, national team coach Heyneke Meyer has already hinted Habana will remain in his plans leading up to the 2015 World Cup.
"In Super Rugby he has looked rather ordinary this season but there is something about Bryan that when you put him in a Bok jersey he's extraordinary," Meyer said recently.
"He is a great player, we go back a long way and he has always played well for me."
Habana still has some way to go to reach the top of the international try-scoring ranks, however.
Japan wing Daisuke Ohata heads the list with 69 in 58 tests, followed by Australian David Campese who grabbed 64 in his 101 appearances in a Wallaby shirt.
Wing Shane Williams managed 58 for Wales and another two for the British and Irish Lions, while current Japan player Hirotoki Onozawa has 55 to date.
Rory Underwood ran in 50 tries in his 91 tests, 49 for England and one with the Lions, a mark matched by Habana in five fewer tests.