The store manager, in a rare show of kindness, reduced my penalty for being late.
The manager unusually showed me kindness and reduced my penalty for being late.
「店長」→「Store manager」か、単純に「Manager」でもいいです。
「やさしさ」→「Kindness」
「減額する」→「To reduce」
「遅刻する」→「To be late」
まとめて言いますと、
「The store manager, in a rare show of kindness, reduced my penalty for being late.」
「The manager unusually showed me kindness and reduced my penalty for being late.」
どちらでも使えます。