The Portland Timbers began Saturday with a chance to clinch their playoff return and stay out in front of the likes of Seattle and Sporting Kansas City in the race to a top-two finish in the Western Conference.

But for the second time in San Jose this season, the Timbers fell flat. Vako opened the scoring in the first half, Danny Hoesen extended the Earthquakes' lead to start the second, and by the time Sebastian Blanco pulled a goal back for Portland late, the game was all but over.

For Timbers manager Caleb Porter, this was a disappointing defeat. At this stage of the season, Porter's best teams have flattened all comers. His 2013 team finished the regular season on an eight-game unbeaten run. His 2015 team won four of its last five to set up its MLS Cup run.

This team, despite the style of its win last weekend, is not there yet. Porter hasn't quite gotten the formula right — and the manner of this loss, leading into a week off for the October international break, has given the coach plenty to chew on.

The Timbers had several significant issues at Avaya Stadium on Saturday night. One was that Earthquakes, humiliated at home 4-1 by the Chicago Fire on Wednesday night, were playing to keep their season alive.

From the first whistle, it showed. San Jose manager Chris Leitch made five changes from the midweek game, and his rested players — especially creators Vako and Jahmir Hyka — spent the first half drifting in and out of channels and creating all kinds of problems for a rather beleaguered-looking Timbers backline.

In the fifteenth minute, the early pressure told when Hyka latched onto a miscued clearance on the left touchline from Roy Miller, skipped past Liam Ridgewell, and picked out Vako — who took one touch into the box, and sent a sweeping shot past Jeff Attinella to give the 'Quakes the lead.

Just more than five minutes later, it was nearly two — Vako this time setting up Hyka on the back post, only for Attinella to make a sprawling kick save.

It was a theme of the first half: the Timbers struggling get significant pressure, struggling to hold the ball, and struggling to stay in the game. Some of that was on the field, some of it might have been on fatigue at the end of a long season, and some of it, undoubtedly, was on the coach.

Despite having David Guzman back healthy, Porter decided to stick with the team that so thoroughly dismantled Orlando last weekend — leaving Miller at left back, Nagbe in central midfield, and Dairon Asprilla on the wing.

It was an understandable decision. Moving Nagbe central was a silver bullet of sorts two years ago, and Guzman hasn't exactly been convincing since the spring. But more than that, the performance last weekend was so good, it was worth seeing if the the players that put it together had an encore in them.

As it happened, they did not. The Timbers missed Nagbe as an outlet for possession on the wing while Asprilla struggled on both sides of the ball and Miller was lit up.

The second half brought no respite. Four minutes after the restart, San Jose doubled its lead on a counter that started when Victor Bernardez — in the midst of a turn-back-the-clock performance of the season — cleaned out Darren Mattocks in the open field, and sent the 'Quakes the other way.

Bernardez got the ball wide to Vako, who slipped the ball into Chris Wondolowski, who fired a pass into the path of Danny Hoesen in the penalty area. Hoesen received the ball in traffic, sharply cut around Roy Miller, and then fired his shot back through Miller's legs and into the far corner for 2-0.

It was a terrific goal from the Dutchman, who, having been stuck on the wing nearly all season, was clearly relishing the chance to play up top.

For Miller, on the other hand, it was another frustrating moment. The Costa Rican has been tremendous for the Timbers this year, but he's been tremendous at center back. At fullback, isolated in space against quick, creative players, the decisiveness that is his best quality disappears.

Take nothing away from Hoesen — or Hyka earlier, or Jefferson Savarino in the RSL game — but if Miller plays left back against good teams, he's going to get exposed. Just ask Red Bulls fans.

Four minutes after the second goal, Porter pulled the plug on his gameplan. Guzman came on for Asprilla and pushed Nagbe to the wing, while Miller was lifted for Vytas. Soon after, Alvas Powell hit the field for the first time in more than a month in relief of Zarek Valentin.

The final forty minutes were by no means rousing, but the Timbers did have a goal dubiously ruled out for offsides before they pulling one back late when Nagbe's excellent, composed work in the penalty area set Sebastian Blanco up to score his first goal since July and make it a one-score game with five minutes to go.

But the comeback would stop there. San Jose, tied on points for the Western Conference's final playoff spot, lives to fight another day. The Timbers, meanwhile, are in a much different spot. They're heading to the playoffs. But it's not quite clear how they should line up when they get there.

For all the good work the Timbers did in August and September, questions abound. Will Fanendo Adi play a part in the season's final month? What is Nagbe's best position? Who plays fullback? Goalkeeper?

Porter has some figuring out to do in the next couple of weeks. Right next to Adi's health, the Timbers' title challenge might ride on his ability to come up with the requisite answers.