Duncan scored 35 points and had 13 rebounds, but did not get enough help from his teammates as the Spurs lost to the Wizards for the first time in eight meetings.
The Spurs trailed, 73-71, entering the final period and Duncan scored their first 10 points.
Hughes hit three foul shots with two minutes left to give the Wizards a 96-86 lead, their largest of the game.
San Antonio responded with five straight points on a jumper from Bruce Bowen and a three-pointer by Steve Smith. But Christian Laettner hit an open baseline jump shot with 1:08 left to give the Wizards a 98-91 lead and Hughes added two more free throws.
Tony Parker, who scored 21 points to lead the Spurs to a 92-81 victory over the Wizards on Dec. 21, fouled out on the play that set up Hughes' three free throws. He had nine points and four assists in 27 minutes.