Wales' 16-6 triumph was their first at Stade de France since 2005 and biggest in the French capital for 38 years.
"It is a pretty special day for the Wales team," interim head coach Howley said.
"We kept on saying we hadn't become a bad team overnight. Fine margins are the difference in Test match rugby.
"The players showed character and our defence put France under a lot of pressure. The players deserve all the accolades."
Wing George North's 73rd-minute try sealed the deal for Wales, while full-back Leigh Halfpenny kicked three penalties and a conversion to end a run of eight successive defeats.
France failed to score a try against Wales for the third successive game - a barren run that includes the 2011 World Cup semi-final in New Zealand - as they were restricted to two Frederic Michalak penalties.
"It was a huge defensive effort - we defended particularly well," Howley added. "We were effective in terms of putting pressure on the ball, and our defence was absolutely outstanding."
The French team were booed off the pitch by a capacity crowd, and they now find themselves propping up the table after losses to Italy and Wales. The wooden spoon is a distinct possibility.
"It is a difficult time for us - we know we can't win the Six Nations any more," France coach Philippe Saint-Andre said. "It was most frustrating. Our defence went better this week, but we had the opportunities to score and did not convert them, whereas Wales scored from their only opportunity.