And after two consecutive wins, the former Wales scrum half faced a selection headache but says Wales should embrace the situation.
"There was a lot of discussion, particularly at seven. We are really fortunate to have two world-class sevens," he said.
"We feel this is the best side to play against Scotland on Saturday.
"We looked at our performance against Italy and we've looked at Scotland and the contact area and breakdown and we just feel that Warby has got a slight edge in that department.
"I've spoken to Justin and Sam and we feel this is the best back-row to go with. Justin has done everything right but we are up against a very potent back-row.
"When you look at Johnnie Beattie, in terms of his carrying, we just feel this is the best back-row to play against Scotland."
Despite Warburton's return to the starting line-up, Ryan Jones leads the side for the third successive game and speaking at today's team announcement, Howley said he sees no reason to change his captain.
"Ryan has been a great leader over the last two or three weeks," he added.
"I explained that situation to Sam. Obviously, he is disappointed. It is about the team dynamics, it is about how Ryan has led.
"Ryan, barring perfomances, will captain against England as well. I just want Sam to go out and concentrate and focus on his own game.
"He is a world-class seven, he has proved that over the last 18 months. He is fantastic in the contact area and at the breakdown and we will certainly need that attribute against Scotland."
With James and Jones returning to a beefed-up Wales pack, Howley's side look to have the bulk to deal with the likes of Richie Gray and Jim Hamilton.
Jones returns to replace the unfortunate Andrew Coombs who, despite impressing in the Championship so far, has to settle for a place on the bench.
"The attributes of physicality and experience will be pretty important on Saturday, particularly in the front-five, Howley said.
"Andrew Coombs can be extremely proud of his performances. He has been outstanding. As I said to him this morning, he couldn't have done anything more and the fact that a British Lion with 68 caps is coming in to replace him I think shows how well Andrew has done.
"Alun-Wyn has been an integral part of this squad over the last few years. I am sure we will use all his experience on Saturday."
You can follow every minute of this week's action between Scotland and Wales at www.wru.co.uk/live just prior to kick-off.