"Apartheid" is a word from Afrikaans and has a history which, as HEIL SATAN points out, has deep associations with South Africa. Be that as it may, you are right to point out that it is in the Rome Convention, although it should also be noted that no country has been convicted of such a crime by the ICC.
However, apartheid is a crime committed within a state's borders - the words "institutionalized" and "regime" are the telltale words here. Apartheid is not a crime committed across international boundaries as there are other crimes, subject to the International Court of Justice, that cover such events.
So, in order to demonstrate that the crime of apartheid existed, one would have to show that a country's regime would, for example
*deny members of a certain group the vote
*deny members of that group the right to work
*deny members of that group the right to citizenship, serve in the armed services, civil service etc.
*deny members of that group equality before the law
*deny members of that group the right to education and healthcare
*deny members of that group the right to buy and sell land
*restrict members of that group so that they had to live in certain areas
All of these factors were true in South Africa. None of them are true about Palestinians living in Israel. While there is plenty to be said about Palestinians living in the West Bank and Gaza, they are not and never have been Israeli territory but much of the West Bank is, and Gaza was, under military occupation. There may be room for a variety of successful claims against Israel here, but not on the grounds of apartheid. Unless Swede is an advocate of Israel's formally annexing the West Bank and Gaza, it is difficult to see how the charge of apartheid could stand.
It is also interesting to see that many of those most vocal in calling Israel an apartheid state were passionate defenders of the apartheid regime of Yugoslavia which, in its behavior toward its own non-Slav citizens, did fulfil all the criteria I listed above.