"Really good luck for the autumn internationals," he said. "I think I'm only going to be here for Aussie game but best of luck for Argentina and New Zealand as well.
"Make sure you win every single one of them," the 28-year-old added.
The charming royal filmed a rousing message for the team while wearing his supporter's shirt against the backdrop of Twickenham stadium.
"You're going to have all the support here, you're going to have 80,000 people in this fantastic stadium, " he said in the short video.
"Make the most of it, everyone's behind you.
"Hopefully the stadium will be filled with white shirts so let's bring it home, make it happen."
The sporty Prince recently showcased his rugby skills during a coaching session with a group of teenagers on Twickenham green.
While Harry showed off his impressive skill set, England World Cup winner Jason Robinson assisted the royal in the training session, and joked that Harry could try out for the national team.
"We're looking for a winger or a full-back," said Jason. "I'll be looking to see what you've got."
"I think I'm a bit past it already," replied a modest Harry.
"It's just fantastic to see him out here with the kids ," said Jason. "He's dripping with sweat. He's put everything into this, because he is passionate about the game."
As patron of the Rugby Football Union All Schools Programme, Harry held the session for state school pupils in the hope of encouraging more students to get into the sport and join their local clubs.
It was not the first time Harry had taken part in rugby training sessions. On his visit to Brazil last year, the fun-loving Prince played a game of rugby in the sand with children from the slums of Rio de Janeiro.