Cano was replaced at second base by left fielder Dustin Ackley, who began his Major League career at second and has played 281 games there, but none since Sept.13, 2013.
Veteran utility man Willie Bloomquist took Seager's spot at third base. Manager Lloyd McClendon said designated hitter Nelson Cruz also was sick before the game.
"We sent Seager home," McClendon said. "He's on an IV bag and medicine. Looking back, I probably shouldn't have played Cruz. He was throwing up as well right before the game. He toughed it out and tried to give us what he had."
Cano has been struggling offensively in his second season in Seattle, hitting .237 with two home runs and 20 RBIs in 64 games. But this was the first time he's been sidelined by any sort of health issue.
"When he came in today his back just locked up on him," McClendon said. "He got it worked on yesterday and was feeling better and today it locked up on him."
Seager, a 2014 All-Star and Gold Glove winner, has batted .272 with 11 homers and 36 RBIs in 66 games. He'd played in 192 consecutive games, the second-longest active streak in the Majors. Atlanta first baseman Freddie Freeman, who held the longest streak in the Majors at 234 games, also sat out Thursday against the Red Sox with a sprained wrist.
The Mariners had a thin bench Thursday with only outfielder James Jones and catcher Jesus Sucre available, even with Cruz playing.
"My hope is that all those guys will be back in there tomorrow," McClendon said. "Right now it's day to day."
Ackley takes ground balls in the infield on a regular basis in batting practice just to keep a feel for things, but acknowledged it was a bit of a surprise to get the late call to his old spot.
"On double plays and all that, it's weird getting back into it after being in the outfield so long," he said. "The throwing is different, just arm slots. It's a whole different ballgame, but it felt better than I thought it was going to so it's something to build from if this happens again."
Greg Johns is a reporter for MLB.com. Follow him on Twitter @GregJohnsMLB, read his Mariners Musings blog, and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.