Eastern Illinois won its own 5K race with 17 followed by SIUE (48), SIU Carbondale (76) and Evansville (92).
"We talked about running as a tight pack, and they executed the plan to put us in a good position," said SIUE Assistant Coach Kayla Brown. "They worked together really well today to place second as a team. It was exciting to see them feed off each other."
Kennedy was the team's top finisher in fifth place in a time of 18:25.84. Miller took sixth overall in 18:34.61. Clarke placed 10th in 18:55.12.
Next up for the Cougars is Sept. 9 when the team travels to Bloomington, Illinois, for the ISU Country Financial Invitational.