Hanowski's goal came moments after Faragher denied Gopher forward Nick Bjugstad on a breakaway.
The Gophers looked to have tied the score with one second left on a two-man advantage when senior Jake Hansen batted a puck past Faragher out of the air, but the goal was disallowed due to a high stick.
Still skating with a one-man advantage, Bjugstad evened the score less than a minute later when his shot from the slot found the back of the net.
The Huskies responded with a power-play goal of their own with 2:40 left in the period when Cam Reid buried a one-time shot from the bottom of the right faceoff circle.
SCSU continued its scoring run in the second period when sophomore center Nic Dowd made it 3-1 at the 4:35 mark and senior winger Jared Festler went against the grain and scored on a feed from Hanowski to put St. Cloud up by three 2:48 later. Festler's goal came on the man advantage.
Minnesota had three odd-man rushes in the final six minutes of the period, but the Gophers missed the net on two of them and saw the other get broken up on a diving play by Sam Zabkowicz.
UM continued to create offensive pressure in the final frame, posting 15 shots in the final 20 minutes, but Faragher kept the Gophers off the board until Tom Serratore buried his third goal of the season from between the circles with 5:01 to go.
Freshman Kyle Rau made it a one-goal game less than two minutes later by swatting home a loose puck in the middle of a goalmouth scrum, but Minnesota was unable to tie the game in the final three minutes.
With the loss, the Gophers fell to 10-3-0 on the season and 7-2-0 in WCHA action. Minnesota still holds a one-point lead in the WCHA standings over Minnesota-Duluth.
The two teams will complete their home-and-home series tomorrow night with a 7:00 game at Mariucci Arena. UM will play another home-and-home series against St. Cloud on Jan. 27 and 28.