Stephane Veilleux also scored as the Wild handed the Blackhawks their eighth consecutive loss.
The Wild, who entered the NHL in 2000-01, posted a franchise-record fourth straight road win. Minnesota has also won four of its last five overall.
Gaborik extended his point-scoring streak to five games, with seven goals and an assist during the span. Friday's game was his seventh after missing 34 with a strained groin. During the streak, Gaborik has had three two-goal games to boost his season totals to 11 goals and four assist in just 14 games.
"I think I was ready when I got back," Gaborik said. "The important thing for me is to warm up and get going. As long as I'm loose and warmed up, I'm OK."
Gaborik opened the scoring in the final minute of the first period on a breakaway, then drove to the net early in the third for his second goal.
"When I started playing, I didn't think about scoring goals," Gaborik said. "I just wanted to get out there and get skating. When I skate, I think things are happening."
Minnesota coach Jacques Lemaire isn't shocked by Gaborik's quick comeback.
"I told you, he's good," Lemaire said. "He's the type of player who can jump on the puck in our end, in the neutral zone or in the offensive zone and get a goal out of it."
Fernandez, who wasn't heavily tested in recording his 13th career shutout, didn't talk to reporters after the game, saying he "didn't feel well."
"I think our forwards did a hell of a job," Lemaire said. "For 2 1/2 periods we were right in their face all the time and skating. That's why we got the chances and we didn't give a lot."
The Wild's road streak has come immediately after Minnesota lost a team-record 11 straight away from home.
"It's big," Minnesota forward Brian Rolston said. "First and foremost, you have to attribute it to the goaltending and secondly getting (Gaborik) back. He's been terrific for us."
The Blackhawks, 0-6-2 in their last eight overall, also lost dropped to 0-5-2 in their last seven at home. Chicago last won the United Center, 2-1 over Dallas, on Dec. 26.
"They had more will than we did," Chicago coach Denis Savard said. "We had maybe two forwards who decided to play a little physical. The rest of them played at the end of their sticks all night long."
The remaining fans for the announced crowd of 12,233 booed the Blackhawks at the end of the game.
"Unacceptable, period," Savard said of his team's performance. "It's says it all when the fans.... We deserved what we got."
The Wild completed a sweep of its four-game season series against Chicago, with three wins coming in overtime or a shootout.
Gaborik scored the lone goal of the first period, completing a breakaway with 24.5 seconds left. Veilleux made it 2-0 with 8:57 left in the second with a shot from the left side of the crease.
Gaborik closed the scoring at 2:39 of the third, as he drove through traffic to the net and converted Wes Walz's drop pass from the slot.
- Four Wild players sat out with injuries suffered earlier in the week. RW Pavol Demitra was out due to an upper-body injury, but was listed as probable for Saturday's game against Dallas. D Keith Carney sat out with back spasms. D Kurtis Foster and C Todd White have lower-body injuries.
- Minnesota D Petteri Nummelin returned after missing 14 games with an upper-body injury.
- Chicago C Peter Bondra missed his second game with a sore left shoulder. Blackhawks D Jassen Cullimore sat out his sixth game with sore shoulder and LW Rene Bourque missed his ninth with a bruised ankle. All three are expected to return after the All-Star break.