Indians catcher Yan Gomes also left the game in the third inning due to illness. Gomes doubled as part of a five-run outburst in the third and was then replaced behind the plate by catcher Roberto Perez in the home half of the inning.
"Abe strained his shoulder on the swing," Francona said. "He's day to day. I don't think it's anything worse than that. Gomer just ate something before the game. Intestinal turmoil. He just wasn't feeling very good."
Utility man Michael Martinez took over in center field for Almonte instead of Lonnie Chisenhall. During Tuesday's win over Toronto, Chisenhall took a pitch off his left index finger on a bunt attempt in the eighth inning. Francona said prior to Wednesday's game that Chisenhall was fine, and he entered in the eighth inning on Wednesday as a pinch-hitter, going 0-for-1.
After the loss, Francona explained that he wanted to keep Chisenhall on Cleveland's depleted bench as a pinch-hitter.
The Indians are also temporarily without left fielder Michael Brantley, who sprained his right ankle on Sunday in Kansas City. Brantley is expected to be ready to return to the lineup on Friday, when the Indians open a three-game weekend series with the Twins.
On the season, Almonte has turned in a .222/.330/.321 slash line in 30 games for the Indians.
Jordan Bastian has covered the Indians for MLB.com since 2011, and previously covered the Blue Jays from 2006-10. Read his blog, Major League Bastian, follow him on Twitter @MLBastian and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.