The 29-year-old had to be taken off in the first half of their 2-1 loss to Real Madrid in the Champions League semi-final first leg on Wednesday and is likely to miss the remainder of the season.
"I see absolutely no danger for the World Cup," Heynckes told reporters. "Quite the opposite, Jerome... will most certainly be at the World Cup. He will be able to train well before it. Even now before the season ends."
The World Cup in Russia starts on June 14 with Germany drawn in Group F along with South Korea, Mexico and Sweden.
Neither Bayern nor Boateng have said how long he is likely to be sidelined with the injury in his left thigh but the 2014 World Cup winner hinted on Thursday his season was finished.
German champions Bayern have three games left in the Bundesliga and travel to Madrid for the Champions League return leg on Tuesday before facing Eintracht Frankfurt in the German Cup final on May 19.
"Life is full of setbacks... Now it's all about fighting to be there in Russia. For the remaining games (of Bayern) I will support my team as much as I can," Boateng wrote on Twitter.
Bayern's Dutch winger Arjen Robben, who also came off injured in their defeat by the Spaniards, is still doubtful for the second leg while David Alaba and Javi Martinez will be fit.
"With Robben we will have to wait. He is relatively fine but with that (thigh) nerve it is difficult to diagnose," Heynckes said.
(Reporting by Karolos Grohmann; Editing by Christian Radnedge)
