This smells like homework, so you can use this working solution if you can explain or re-write it.

 echo "Student Id Class
John 23 2
Mark 33 3
Jerry 44 2
Sam 55 2
Tom 65 3
" | perl -ane '$F[2]=~/^\d+$/ or next;push @{$h[$F[2]]},$F[0]}{ $h[$_]
+ && print qq|Class $_ = |,join(",",@{$h[$_]}),qq|\n| for 0..$#h'
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Output:

Class 2 = John,Jerry,Sam
Class 3 = Mark,Tom
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UPDATE: FWIW, the Data structure used in the code above is an "Array of Array(ref)s".
The code posted below this node uses a Hash of array refs.