Werner made 10-14 from the field, part of the Eagles' 59.2 percent shooting from the field. Chris Ask added 15 points on 5-6 from the field and like Werner was 4-4 from the line. Timothy Owen made all three shots from the field and 7-8 free throws to finish with 14 points.
Mark Gossens led the Pioneers with 23 points, one shy of his career high, while LeVon Crawford scored 15 and Jeff Skemp 10 for the Pioneers, who connected on 47.9 percent from the field.
The Eagles improved to 7-1 overall and 2-1 in the Wisconsin Intercollegiate Athletic Conference, while the Pioneers dipped to 4-4, 0-2.
UW-La Crosse led 32-26 at the half, but the Pioneers tied the score at 44-44. Jeff Skemp made six straight free throws, and Charlie Lohoff scored a layup to lead the Pioneer charge. Werner, however, made back-to-back inside shots, and the Eagles never trailed again.