Josef Martinez and Franco Escobar scored either side of half-time at a sold-out Mercedes-Benz Stadium in Georgia.
It capped a fine campaign for Gerardo Martino's men, who were largely in control throughout against the Timbers in the coach's final game in charge.
The season finale took a while to get going, with Martinez having a penalty shot turned down in the opening stages.
Darlington Nagbe and Miguel Almiron, the latter forcing a good save from Jeff Attinella, had opportunities for Atlanta before the opener.
Michael Parkhurst's sliding tackle saw the ball fall to Martinez, the prolific MLS MVP calmly rounding Attinella before opening the scoring six minutes before half-time.
Portland looked for an immediate response and Jeremy Ebobisse had a header saved by Brad Guzan prior to the break.
The Timbers also looked the better side after the interval, with David Guzman putting a good chance over the crossbar from close range.
Instead, Atlanta doubled its lead in the 54th minute.
Almiron's set-piece was met by Martinez, whose flicked header fell to Escobar to put away at the back post.
Portland continued to struggle to create much of note, while Martinez headed straight at Attinella at the other end as Atlanta saw out a deserved win.