Crew goalkeeper William Hesmer leaped to stop Brunner's header off a cross from Kalif Alhassan in the 46th minute but the ball bounded into the net.
Brunner spent the previous two seasons in Columbus before he was selected by the Timbers in the second round of the 2010 Major League Soccer expansion draft.
The expansion Timbers (5-3-2) are the only team in MLS to win all of its home games.
The announced crowd at Jeld-Wen Field was 18,627, a sellout.
The Crew (3-3-4) have yet to win on the road this season.
The Timbers were coming off a 1-all draw with the rival Sounders in Seattle last Saturday. Portland pulled even with the Sounders when Jack Jewsbury's free kick caromed off the head of Futty Danso and into the net.
The Crew were coming off a 3-0 loss to the San Jose Earthquakes last Saturday. Columbus was undefeated in its previous seven games.
The Crew have three losses and a trio of draws on the road this season.
Perkins made three saves in the match.
Crew forward Emilio Renteria was injured early in the match and was replaced by Andres Mendoza. The nature and extent of his injury was not announced.
Alhassan leads the Timbers with five assists, and defenders have scored five of the team's goals this season.
The Timbers Army, Portland's independent supporters' group, unfurled a banner reading "Raptured," for the match, noting the doomsday prophesy for Saturday night.
No other expansion team has won its first five home matches in MLS history. And no team overall has won as many home games to open a season since the Los Angeles Galaxy won their first seven in 1996.
According to information provided to the Timbers by the Elias Sports Bureau, no other expansion team has won as many consecutive home games since the Chicago Fire won seven straight and the Miami Fusion won six straight in 1998.