Manoah's suspension begins Saturday, making the 23-year-old eligible to return on July 2.
The decision comes after Manoah pitched six innings in Friday night's 6-5 extra-innings loss to Baltimore, allowing four hits and no earned runs while striking out six batters and walking a pair.
Manoah was ejected in the fourth inning against the Orioles on June 19 after hitting Franco. Following the play, an umpire escorted a visibly upset Franco away from Manoah, who was walking toward home plate. Both benches cleared soon after but cooler heads would prevail.
Manoah told reporters after the game that he didn't intend to hit Franco and that the pitch "slipped away."
On Tuesday, both the rookie pitcher and Blue Jays manager Charlie Montoyo were disciplined for the incident. Manoah was suspended five games – which he said he planned to appeal – while Montoyo served his one-game ban during that night's game against the Miami Marins.
In six starts for the Blue Jays this season, Manoah sports a 3.34 ERA and 1.112 WHIP with 33 strikeouts and 11 walks across 29.2 innings.