The Fire had taken the lead after just 19 minutes when Norberto Paparatto barged into the back of Quincy Amarikwa in the box, which allowed Jeff Larentowicz to score from 12 yards out on the ensuing penalty.
Portland pushed in search of a tying goal and came close in the 71st minute when Will Johnson eluded Sean Johnson only to send his effort inches wide of the open net.
But the Timbers eventually leveled the score 11 minutes from time when Darlington Nagbe's shot was stopped by Johnson but directed to the feet of Fernandez, who turned in the rebound from close range.
Fernandez has made an impactful start to life in MLS, scoring a total of two goals in his first two games with the Timbers. The Argentine newcomer's last- gasp goal at Providence Park last week helped Portland steal a point in a 1-1 draw with the Philadelphia Union.
The Timbers will hit the road next time out for their first match away from Providence Park this season, taking on the Colorado Rapids at Dick's Sporting Goods Park on Saturday.
Chicago, meanwhile, will enjoy its first home match of the season when it welcomes Red Bull New York to Toyota Park on March 23.