It sounds like you want a relabeling rule like:
relabel_configs:
- action: replace
source_labels: [__meta_kubernetes_pod_container_name, __meta_kubernetes_namespace, __meta_kubernetes_pod_container_port_number]
target_label: instance
regex: (.+);(.+);(\d+)
replacement: $1.$2:$3
(The source labels are concatenated with a ";" by default for the regex match - you can control this character by setting "separator: ..." explicitly in the relabeling rule)
Be aware that the combination of pod container name, namespace, and port number doesn't necessarily give you a unique instance identifier, as there could be multiple pods with the same attributes. If you have multiple pods of the same type, you probably want some distinguishing label like "__meta_kubernetes_pod_name" or so in there. Most commonly, the labels that identify a type of instance rather than a single specific instance / pod, are put into the "job" label instead (with sometimes some dimensions like namespace etc. broken out into separate labels as well).