Only one run came home on a hit.
The Yankees, who will remain in Chicago to play the White Sox, had 13 hits in the game -- all singles -- and snapped a two-game slide.
The Cubs had a three-game winning streak snapped, which included a 6-1 win in the series opener on Tuesday when they became the first major league team to beat Yankees rookie Masahiro Tanaka.
They continued to let down Samardzija, who has now gone 16 starts without a win, including 10 outings this season, despite leading the majors with a 1.46 ERA.
Notable deaths of 2014 [PHOTOS]
LeBron James reveals his new Nike shoes