Rochester (19-4 overall, 8-4 UAA) fell behind 53-49 when Nofi Mojidi hit a three-pointer with 4:41 left in the contest.
The Yellowjackets then scored the game's next seven points, capped by a jumper by Megan Krebbeks, to take a 56-53 lead at the 2:09 mark. Krebbeks finished with 10 points.
Chicago (17-6, 6-6) took its last lead, 57-56, on a three-point basket by Alex Leach with 1:10 to go, but a Muller basket 19 seconds later put Rochester ahead to stay, 58-57.
Leach sunk a pair of foul shots with nine seconds left to pull the Maroons to within a point, 60-59, but Alex Porter hit two free throws one second later to increase the Yellowjackets' edge to 62-59.
The Maroons had a chance to tie the game in the final seconds, but their 26th turnover of the game handed the ball back to Rochester. Muller, who paced the Yellowjackets with 14 points, sealed the win as she converted a pair of free throw attempts with two seconds left.
Korry Schwanz led all scorers with 15 points for the Maroons, while Jill DiNucci added a career-best 13 off the bench on 6-of-8 shooting.
Losing for the first time in 18 games when leading at the 5:00 mark, Chicago suffered its second straight setback and sixth in its last seven outings.
Julie Marriott added 13 points for the Yellowjackets, who improved to 10-0 at home despite committing 29 turnovers.
ROCHESTER 64, CHICAGO 59 CHICAGO (17-6, 6-6 UAA) Schwanz, Korry 5-11 4-4 15; DiNucci, Jill 6-8 1-2 13; Hackney, Molly 2-7 5-6 9; Leach, Alex 2-5 2-2 8; Mojidi, Nofi 2-15 1-2 6; Rapier, Nicaya 1-3 2-2 4; Stinson, Jamie 1-4 0-1 2; Woods, Anna 1-1 0-0 2; Tanaka, Lori 0-0 0-0 0; Devaney, Kaitlin 0-0 0-0 0. Totals 20-54 15-19 59. ROCHESTER (19-4, 8-4 UAA) Muller, Danielle 5-6 3-4 14; Marriott, Julie 5-10 3-5 13; Krebbeks, Megan 4-6 0-0 10; Bango, Emily 2-6 4-5 9; McNelis, Johanna 2-3 1-2 6; Waddell, Jessica 3-6 0-0 6; Lyons, Emily 2-5 0-0 4; Porter, Alex 0-2 2-2 2; Mastronardi, Jessica 0-1 0-2 0; Fisher, Marlena 0-0 0-0 0; Baroody, Helen 0-4 0-0 0. Totals 23-49 13-20 64. Chicago....................... 28 31 - 59 Rochester..................... 26 38 - 64 3-point goals-Chicago 4-14 (Leach, Alex 2-4; Mojidi, Nofi 1-5; Schwanz, Korry 1-3; Stinson, Jamie 0-2), Rochester 5-14 (Krebbeks, Megan 2-4; Bango, Emily 1-3; Muller, Danielle 1-1; McNelis, Johanna 1-2; Mastronardi, Jessica 0-1; Baroody, Helen 0-3). Fouled out--Chicago-None, Rochester-None. Rebounds-Chicago 30 (Rapier, Nicaya 9), Rochester 32 (Bango, Emily 7; Marriott, Julie 7). Assists-Chicago 11 (Leach, Alex 3), Rochester 18 (Bango, Emily 8). Total fouls-Chicago 18, Rochester 15.