Ortiz was benched indefinitely a day after he went 0-for-7 and stranded 12 base runners in an extra-inning loss at the Los Angeles Angels. Ortiz has gone 144 at-bats since his last home run on Sept. 22 against Cleveland's Zach Jackson at Fenway Park.
Though available as a pinch hitter, Francona did not give Big Papi a chance to end the drought one at-bat shy of matching the longest dry spell for homers in his career.
Chris Jakubauskas (2-4) survived allowing four runs -three earned - and nine base runners in the first three innings to last six innings. He gave up seven hits for his first career win as a starter
- on his sixth try. Sean White and Mark Lowe pitched two scoreless innings behind the 29-year-old former shoe salesman.
Then David Aardsma, discarded by Boston in a trade after last season, gave up a two-out single to J.D. Drew, who had three hits replacing Ortiz as Boston's No. 3 hitter, before getting Jason Bay to fly out at the left-field wall for his fourth save in four chances. Aardsma is taking over for demoted closer Brandon Morrow.
Seattle won for just the second time in 11 games.
Boston lost its third straight on its final West Coast swing of the season.
Ellsbury doubled, tripled and beat out an infield chop for a single in his first three at-bats while the Red Sox built a 4-0 lead.
Rocco Baldelli struck out three times while replacing Ortiz as the designated hitter.
Lester (2-4) took a 4-1 lead into the sixth and Yuniesky Betancourt hit a potential inning-ending double-play one-hopper back to him. But Lester double-pumped and never threw to second base. He settled for the out at first.
Franklin Gutierrez followed with a two-run single to make it 4-3, Seattle's first hit in 11 at-bats with runners in scoring position.