Despite an astonishing 28-5 advantage in shots, Sounders FC managed just one goal after 90 minutes Wednesday against Panamanian club San Francisco FC.

Besides a lone strike from midfielder Alvaro Fernandez in the first half — which tied the two-game CONCACAF Champions League preliminary round matchup at 1-1 — each miss was followed by another confounding miss, ultimately sending the series to extra time.

But despite the offensive frustration, Seattle persevered and prevailed in front of 21,233 fans at CenturyLink Field.

Nate Jaqua scored the winner in the eighth minute of extra time to give the Sounders a 2-0 win on the night and a 2-1 aggregate-goals advantage after playing twice, home and away.

"When you're coming off a series of games where you haven't gotten the results, sometimes it seems like that win that gets you back over the hump is one of those where you grind it out," said coach Sigi Schmid, whose team snapped a two-game losing streak in all competitions. "It wasn't necessarily a thing of beauty — even though we created a lot of chances, so there's a little bit of frustration there — but our character showed through at the end."

Seattle, which came in having to overcome a one-goal deficit after San Francisco FC won the first leg 1-0 last week in Panama, will play in the CCL group stage for a second straight year.

Dozens of scoring chances in regulation only accounted for one Sounders FC goal, and once again the head of Fernandez came up big in the preliminary round.

One year after clinching qualification into the CCL group stage with a crucial header in El Salvador, the Uruguayan midfielder headed in the series equalizer Wednesday in the 41st minute off a Leo Gonzalez cross.

"We needed that goal," said Schmid.

Fernandez had earlier chances — in the second, 24th and 35th minutes — but all narrowly missed, the last of which forced the designated player to clench his jersey in his fists and scream in anger.

"Truth is, I was getting a little bit disillusioned ... but the good thing about soccer is it gives those opportunities back to you," said Fernandez through a translator.

Such was the tenor of the night, but Jaqua would seal the win later, receiving a cross from Fernandez at the far post and calmly finishing the wide-open chance in extra time.

"It was nice to see it go in," said a smiling Jaqua, who was hoping to atone for an 81st-minute miss.

Sounders FC dominated early and often, outshooting the visitors 12-4 in the first half with a 7-0 advantage in corner kicks.

As lopsided as the play was, San Francisco nearly took a stunning two-goal series advantage in the 12th minute, but Seattle goalkeeper Kasey Keller was just able to redirect a dangerous shot by Rolando Algadona with a phenomenal reflex save, keeping the Sounders in the game.

"Probably one of the turning points of the game," said Schmid.

Seattle qualified for the CCL by winning the 2010 U.S. Open Cup and advances to a difficult Group D, headed by defending champion Monterrey of Mexico. Guatemalan club Comunicaciones is also in the group, and the fourth will likely be Herediano of Costa Rica, which beat Guyana's Alpha United FC 8-0 in the first leg of their preliminary-round pairing.

Notes

• Sounders FC next goes on the road for a 5:30 p.m. MLS game Saturday against Sporting Kansas City.

• San Francisco FC, the 2011 Clausura league champion, won the first leg of the series 1-0 last Tuesday on a 28th-minute penalty kick by veteran forward Roberto Brown. The Monks had qualified for the CCL preliminary round four seasons in a row.

• Seattle will host Comunicaciones on Aug. 16 at 7 p.m. in the first CCL group-stage game (midfielder Osvaldo Alonso will be suspended due to yellow-card accumulation). The Sounders then go to Monterrey for a 5 p.m. road game on Aug. 22. The rest of the group-stage schedule has yet to be announced.

Joshua Mayers: 206-464-3184 or jmayers@seattletimes.com