Dwayne De Rosario converted a penalty in a frantic stoppage time period which also saw a red card for captain Henry.
De Rosario returned to the New York lineup after Canada's elimination from the Gold Cup and immediately made an impact, feeding Austin Da Luz from the left wing for a goal in the fifth minute.
Portland equalised with Jack Jewsbury's hard strike from the top of the box in the 48th minute. Two minutes later, the Timbers took the lead through a goal from former Red Bulls defender Kevin Goldthwaite, making his first appearance since March.
The Timbers took a 3-1 lead on an own goal by former Timbers defender Stephen Keel in the 68th minute.
Henry narrowed it to 3-2 in the 73rd minute, touching off a brief scuffle between the two teams. The former France striker moved level with Landon Donovan of the Los Angeles Galaxy for most goals in MLS this season. He was sent off in stoppage time for an off-the-ball incident.
Portland had a chance from the spot to restore its two-goal lead, but Jewsbury's penalty rebounded off the right post.
A short time later, De Rosario converted the equalizing penalty which was awarded for a Rodney Wallace handball.
Portland was without coach John Spencer, who was suspended for a match because of comments he made about the officiating following Portland's 1-0 loss to the Colorado Rapids last weekend.