Use the formatted printing function, like
> awk -F, '{$4 = sprintf("%02d:%02d", int($4/60), $4%60)}1' OFS=, file
"jone","spdb-deploy","SD",00:25
"abrham","Data-deploy","DD",00:05
"crater","aps-deploy","AD",00:25
"valu","Platform-deploy","PD",00:05
"kiol","teer-deploy","TD",03:00