Hi
You might want to keep the following rule in mind regarding the use of fewer and less.
Rule'Less' is used with uncountable nouns. E.g. - less water, less happiness, less money, etc.
'Fewer' is used with countable nouns. E.g. - fewer cards, fewer people, fewer companies, etc.
Now, coming back to your question:
In sentence 1, 'fewer' is modifying 'intelligent students' and not just the adjective 'intelligent'. Hence it's basically saying that I have fewer number of intelligent students in my class (say 2 out of 10 students)
In sentence 2, 'less' is only modifying the adjective 'intelligent' and is basically saying that students in my class have a lower intelligence level in general.
This is a perfect example of how the meaning of a sentence changes when you actually think that both the sentences sound/mean same.
Hope this is helpful.

Cheers!