I forgot - you originally said 3.5", meaning you have only the capacity for two disks ... when you said "OMSA under Physical Disks both hard drives are "no" under hot spare", I thought you meant the two new disks you put in (newer 1950's can take four 2.5" disks). Yes, you will need to replace each one, allowing the first to completely finish rebuilding before replacing the other. NEVER power down a server to replace a failed hot-swap drive.  Do it "hot".
Hello, I have an old PowerEdge 1950 with PERC 5/i. I would like to replace the two RAID 1 3.5 SATA hard drive with a new ones and I would like to ask if there is a way to replace the first one and let PERC rebuild the mirror and then replace the second one and let PERC rebuild the mirror again? Guided steps will be much appropriated.  Kind Regards, Asaf 
How to replace hard drives?