Doubts had been raised about the tour after Chelsea said they would not travel without manager Avram Grant and defender Tal Ben-Haim.
Malaysia does not have diplomatic relations with Israel, and citizens need special permission to travel to the country, but foreign minister Rais Yatim said there would be no problems with the Chelsea pair.
Rais told the official Bernama news agency: "In this case, although we don't have diplomatic relations with Israel or direct trade with the country, we don't have objections over their visit.
"They are a sports team with two Israeli members. We don't see it as something wrong.
"We have to look at this on a case-by-case basis. We don't want to mix politics with sports."
Chelsea are due to play the Malaysia national team in Kuala Lumpur on July 29.