EMU (21-12) closed on a 6-0 run while holding fifth-seeded Bowling Green (20-11) scoreless for the final 4:46. Anthony Henderson scored the Falcons' final points to tie it at 67.
Lee put the Eagles ahead for good with a pair of free throws 13 seconds later. Talley and Olalekan Ajayi added two more free throws each and Eastern Michigan advanced to a third-round matchup with No. 4 seed Toledo on Thursday.
Karrington Ward added 15 points and 10 rebounds for EMU, which had 18 offensive rebounds and only seven turnovers to get 14 more field-goal attempts than Bowling Green.