The players -- all-America cornerback Trumaine Johnson and backup quarterback Gerald Kemp -- were arrested on charges of disturbing the peace and obstructing police, The Missoulian newspaper reported.
Missoula police Sgt. Collin Rose said the players, both 21, were shot with stun guns to help officers subdue them during a struggle.
The incident happened after the Montana squad had returned from a Saturday win at Northern Arizona University.
"We are continuing our investigation into the allegations, and will let the judicial system run its course," Montana Athletics Director Jim O'Day said in a statement. "Any disciplining will be handled internally through our student-athlete code of conduct."
The newspaper said the incident happened about 2:40 a.m. at an off-campus party attended by about 30 people.