The pain of those narrow losses is not easily forgotten and Howley knows it will push his players onwards and upwards when they face Argentina, Samoa, New Zealand and Australia once more at the Millennium Stadium in November and December.
"Of course it's niggled," said Howley of the memories of those narrow defeats in Tests two and three in particular.
"It's about fine margins with big consequences and it's a series you look back on, not only in terms of statistics, but you've got a gut feeling, both as coaches and players, that we could have won that series 2-1.
"It didn't happen and you use that as motivation.
"I said to the players in the changing room after the third Test, 'Just remember this time and keep it in your belly and make sure that you use it internally, however you want, going into the autumn series."
Howley expects a tough challenge from all four of Wales' opponents this autumn and he is aware that the Grand Slam Champions will need to keep their nerve at key moments if they are to be more successful than they were in the summer.
The Wallabies did exactly that on home soil and Howley is hopeful his side can mirror that mental toughness and execution under pressure when the southern hemisphere sides arrive in Cardiff.
"It's about holding our nerve, mastering the moment when you get into the lead, remaining with our emotions intact," added Howley.
"When we've got five or six minutes left in a game, we've got to be accurate under pressure and have the basic skills under pressure to carry the result.
"Because we have put ourselves in positions - in the first, second and third Tests - to win those games against Australia."
Whatever happens in terms of results in the four back-to-back internationals that begin against the Pumas on November 10, Howley is certain that his players won't lack the desire and determination to do their country proud again.
"To wear the national jersey is pretty important to these guys and their attitude was fantastic for four weeks on tour.That will be the same when they come back for this autumn."