Warburton, 23, sustained a shoulder-nerve injury in Wales' final match of this year's RBS 6 Nations against France, making him a doubt for the Red Dragons' three-Test tour in June.
Although Warburton only played 80 minutes once during the 2012 Championship, against England in a 19-12 victory at Twickenham, Howley insists his presence on tour will significantly boost Wales' chances of beating Australia in their own back yard.
"The decision has been made on Sam," said Howley.
"He is going to be our captain in Australia.
"His rehab has gone particularly well and I have checked with the medical staff and spoken to Sam himself.
"He is very comfortable with where he is. He has started conditioning work and is showing great strides.
"He trained with Leigh Halfpenny last Thursday and Friday and it doesn't look as if he's been away too long.
"Having seen his predicament over the last couple of months, it's great to see Sam smiling and looking forward to the Australia tour.
"It is so important for him to lead us because he has been so impressive as a captain over the last 12 months. His captaincy credentials are there for all to see.
"He was fantastic at the World Cup and he led from the front during the Six Nations campaign.
"We are very much looking forward to him joining us."