The Harlequins forward has been chosen ahead of the more experienced Tom Wood, who has recovered from the shoulder injury he sustained against France on Saturday and will take his place on the bench.
England also beat France with a late try in their opening match of the Six Nations last week at Twickenham.
James Haskell is again named on the bench alongside Wood but with Chris Robshaw and Billy Vunipola already sidelined through injury, it leaves Clifford, Maro Itoje - who makes only his second global back-row appearance - and Nathan Hughes comprising the back row.
Opposing them are Justin Tipuric, Sam Warburton, and Ross Moriarty, who share 130.
Maybe it will come down to a Leigh Halfpenny-Owen Farrell goalkicking contest but there's no question, the stakes have gone up a notch for this annual grudge match.
"I think the quality and experience in that back-row will have a significant impact on the game at the weekend".
"Unfortunately, England know how to win".
After naming them in his side, Howley says that they will live the final decision about the key duo until matchday.
Jones continued to fan the flames in the build-up to the clash in Cardiff this weekend after stating earlier in the week that he can not understand why England's record in Wales is so "horrendous".
They hoped to make England freeze, but Chris Robshaw got into a standoff with officials and refused to leave the tunnel until Wales came out at the same time.
Italy made four changes to their team for the Six Nations match against Ireland in Rome tomorrow, with lock Andries Van Schalkwyk and flanker Simone Favaro, who were left out of the opener against Wales, set to return to the starting lineup.
The England coach had previously dismissed the roof played any part in his preparation for the match, saying: "I'm not an entertainer - I'm a coach". "Every game for us is important and our supporters, and Wales is our next game so it's the most important".
Eddie Jones called in expertise from some unconventional sources yesterday when England football manager Gareth Southgate visited Jones's team in training at Pennyhill Park. If you're loose against this lot, they sniff it. We have a young team eager to play well at the great Principality Stadium.
Victory for England would make it their ninth Six Nations win in a row, equaling their longest ever streak since Italy joined the competition (nine wins, 2002-2004).
Howley said fly-half Dan Biggar's display was one of the highlights for Wales.
"We have prepared for any shenanigans that might go on". Scotland took their red-hot club form onto the worldwide stage last weekend to kickoff their RBS 6 Nations campaign with a 27-22 triumph over Ireland.