The second-seeded Davydenko captured the 15th title of his career and became the first Russian to win the clay-court tournament. Mathieu, the 13th-seeded Frenchman, was playing his first final of the year.
Davydenko last won a title in Warsaw 13 months ago. Injuries forced him to miss close to four months at the start of the season.
The 28-year-old Russian fell behind 3-1, but won five of the next six games to clinch the set. Mathieu gained an early break in the second, only to see Davydenko storm back to win the final five games.
Davydenko hit 78 percent of his first serves and converted five of his 13 break points.