Both players were absent from Sunday's game against the Pacers as well.
Lowry, who also missed Friday's win over the Miami Heat, has been dealing with what the team described as a right foot injury.
Siakam was sidelined yesterday with left knee swelling. During the Raptors' win against the Miami Heat, Toronto's young star was experiencing what had been described as a groin injury. It is unclear at this time if the injuries are connected.
In 13 games this season, Lowry is averaging 18.2 points and 7.1 assists.
Siakam, after struggling to start the year, has averaged 18.6 points, 8.1 rebounds and 4.7 assists in 14 games.
Without Lowry and Siakam in the lineup, Toronto won its Sunday game against the Pacers 107-102, improving to 7-9 overall on the season.