Scherzer, a three-time Cy Young Award winner and seven-time All-Star, originally experienced back stiffness against the Detroit Tigers on June 30. The ace worked through the ailment Saturday against the Kansas City Royals, striking out 11 over seven shutout innings.
After the game, Scherzer began to experience back stiffness again, leading him to pull out of the Midsummer Classic.
"Our season matters so much more than the All-Star Game," Scherzer told reporters. "I know my body pretty well. I just know I'm not going to be at my best if I try and pitch on two days' rest and I'd really be jeopardizing our season if I were to try and do something like that."
Scherzer has a 9-5 record with a 2.30 ERA and 181 strikeouts across 129 1/3 innings this season. Behind the All-Star pitcher, the Nationals, who began the season with a 19-31 record, have rallied to get back into the NL East race.
This year's MLB All-Star Game takes place Tuesday night at Progressive Field in Cleveland.