Even when it was time to say goodbye, the two were still holding each other.
Literal
Part time [at-に] become-even two-people [topic-は] embracing were.
別れるときになっても uses ~ても to express 'even when it became time to part.' 抱き合う is a reciprocal verb: 'to embrace each other' (抱く + 合う). The ~ていた places the embrace as an ongoing state in the past. An emotionally vivid scene.