He did not play in the opener of the three-game series against the Washington Nationals on Friday night, a 6-5 Toronto win, and he is not expected to play in the second game on Saturday at the Rogers Centre.
Scherzer is 4-1 with a 2.15 ERA in eight career starts against the Blue Jays.
A sixth-round draft pick by the Nationals in 2005, Estrada is 2-1 with a 4.34 ERA in six career starts against Washington.
Meanwhile, Yangervis Solarte, the player who often fills in at third for Donaldson when he is not playing shortstop or second base, did well Friday night.
Solarte hit two home runs against the Nationals -- a two-run shot and a solo blast -- and added a double. He became the ninth Blue Jays batter to hit home runs from each side of the plate in a game. It is the second time in his career that the switch-hitter has homered from each side of the plate in a game. He has 14 homers and 40 RBIs for the season.
By defeating Washington starter Gio Gonzalez, who allowed a season-high five runs in six-plus innings, the Blue Jays ended a streak of 11 straight losses when opposing a left-handed starter. It was the longest such streak in franchise history. Their previous long drought against left-handed starter was eight losses in a row in 1993.
Donaldson was eligible to return from the disabled list a week ago but has not played because he has been unable to run well enough during drills at the Rogers Centre on Thursday, an off-day in the schedule.
"I was here watching him (Thursday) when he was running the bases, and he still couldn't cut it loose," Blue Jays manager John Gibbons said. "That's all I've got. He's feeling better, but he's still a little bit hesitant."
He has been on the DL since May 29. The Blue Jays are 6-9 in the games he has missed. He probably will need a rehabilitation assignment at Triple-A Buffalo before returning.
"I think he needs to go down and at least play a game and test it," Gibbons said. "Game-like conditions. I think that would be smart."
The Nationals lost first baseman Matt Adams when he took a pitch off his left index finger on a foul bunt attempt in the second inning. He finished the at-bat and struck out. He played in the field in the bottom of the second before being replaced by Mark Reynolds. The finger was swollen and will be re-evaluated Saturday.
"It's just part of the game, stuff like this happens," Adams said. "Come in tomorrow and get some treatment and see how it feels."
The Nationals did have some good news from the game Friday. Daniel Murphy picked up his first hit of the season, an RBI single in the eighth. It was his third game after being sidelined following right knee surgery.
The Nationals came back Friday with two runs in the eighth after falling behind 6-3 in the seventh and had the potential tying run at third in the ninth.
"I like the way that we didn't give up, came back, and we had a chance to tie the game at the end," Nationals manager Dave Martinez said.