However, England's FA said Ezri Konsa, Kobbie Mainoo and Morgan Gibbs-White will miss the games against Greece and Finland through injury.
Kane, who has scored 10 goals in eight games across all competitions for the Bundesliga club this season, was competing for a ball when he clashed with an Eintracht Frankfurt player and collapsed to the ground grimacing in pain.
Bayern physios could be seen treating his right leg before he was taken off in the second half of the 3-3 draw with Eintracht Frankfurt over the weekend.
Bayern said Kane travelled directly from Frankfurt to England on Monday and FA medical staff examined the 31-year-old on arrival.
"All-clear for Harry Kane," Bayern said in a statement.
"The examination by the England football team medical staff has shown that Harry Kane does not have a structural injury.
"The FC Bayern striker, who was substituted in the Bundesliga match at Eintracht Frankfurt ... will therefore remain with the England squad for the upcoming internationals."
Aston Villa defender Konsa suffered a hamstring injury just 12 minutes into their 0-0 Premier League draw with Manchester United on Sunday.
Mainoo missed Manchester United's Europa League 3-3 draw with Porto on Thursday because of an injury concern, but returned to play against Villa on Sunday and was substituted in the 85th minute.
Gibbs-White picked up an injury in Nottingham Forest's 1-1 draw at Chelsea on Sunday.
"No further additions planned at this time," the FA said in a statement.
England play Greece at Wembley Stadium on Thursday (Friday AEST) in the Nations League, and face Finland three days later.
