Oregon (8-2) opened with a run in the first, but heavy showers delayed action for one hour and two minutes.
The Ducks tacked on a second run when play resumed, and held the 2-0 lead until the fourth when Cal-State Fullerton took the lead behind three runs.
Aaron Payne, who acted as the Ducks first run of the game, brought home Connor Hofmann on a RBI single to tie it in the fifth. But the deadlock was lifted on the Titans second extra base hit of the game, a solo home run to left center by J.D. Davis off of reliever Stephen Nogosek.
"I thought we had quality at-bats, but we just didn't come through yesterday or today," left fielder Kyle Garlick said. "They had more timely hitting than us this series. I think that's why we lost.
The hit was just the second off of Nogosek who replaced Porter Clayton for 3.1 innings of solid relief work.
Clayton struggled with his command in the less than favorable conditions, walking five batters following the first inning, before leaving down 3-2 in the fourth.
"Losing the series simply came down to giving them too much," Horton said. "Yesterday and today it was just the case of not throwing the ball over the plate. You can't give good teams free base runners."
Oregon walked eight batters Sunday and 13 total for the weekend.
Clayton's first start of the season was not what he had hoped. The sophomore is in a multiple pitcher battle for the third and final spot in the weekend rotation.
He allowed three runs on nine base runners.
Both sides scored in the ninth inning. Payne acted as the tying run, but ended the game when he was caught stealing second base.
"We were trying to get in scoring positing and give us a chance to tie it with J.B. You've got to gamble and take chances if you want to win," he said following the loss.
The Duck's first run was unearned, coming after Payne slapped a hard-hit ball to left field that was bobbled and dropped by left fielder Greg Velazquez. Payne reached third on the gaff and was brought in by Tyler Baumgartner two batters later.
Oregon managed eight to outhit the Titans 8-to-7 in the loss. Payne led the way with a 3-for-5 2 RBI performance. He was involved in three of the four runs.
Cal-State Fullerton led off six of the nine innings with a base runner.
The first pitch was delayed 17 minutes due to conditions.
The Ducks have now lost three straight after winning their first eight games of the season.
"One of my favorite quotes is a Lombardi quote, 'Real glory is getting knocked to your knees and coming back'. We got knocked to our knees," Horton said.