The Villans will head home to finish their pre-season preparations after remaining unbeaten during their time in the United States thanks to American keeper Brad Guzan's heroics
Ciaran Clark and Matt Lowton twice gave Villa the lead from corners but efforts by Sebastian Rincon and Rodney Wallace pegged them back.
Paul Lambert saw all five of his penalty takers find the net, with Brad Guzan proving the hero as he saved the Timbers' final effort, taken by Bright Dike, from 12 yards before Samir Carruthers converted the decisive kick.
Summer signings Lowton, Brett Holman and Karim El Ahmadi were included in Villa's starting line-up, which saw Andreas Weimann and Nathan Delfouneso paired in attack, while former Middlesbrough striker Kris Boyd started for the MLS side.
After Stephen Ireland saw an effort ruled out for offside and Holman fired another just wide, it was Clark who gave Villa a deserved advantage, nodding home from five yards out.
Despite a raft of substitutions, Villa were still playing fluently and they were unfortunate to see the linesman's flag raised again after Delfouneso stroked home following some neat build-up play from Ireland and Charles N'Zogbia.
The Timbers hit back, however, as Ryan Kawulok flicked on a corner for Rincon to prod home from close range.
Paul Lambert's side regained their lead late on from a corner off their own. Barry Bannan's whipped cross was cushioned by Nathan Baker for Lowton to smash past the goalkeeper.
With a win seemingly secured the Villa goal scorer and former Sheffield United man was then unfortunate to see Wallace's late effort deflect off him and loop into the net.
Level after 90 minutes, the match was decided on penalties, with the first eight takers all finding the net.
Guzan stood firm to deny forward Dike from the spot before Carruthers stepped up to score the winning effort.