The Norwegian named a strong starting line-up after replacing Neil Lennon in the Hoops dug-out, with Kris Commons, Stokes and Virgil van Dijk all included from the off in a pre-season clash at the Hofmaninger Stadion in Wimsback.
The Scottish champions made a swift start as Republic of Ireland forward Stokes lobbed home the opener after just 70 seconds.
Centre-half Charlie Mulgrew's slip-up then let in Odil Ahmedov to level after 20 minutes but Celtic regained the lead six minutes before the break when a mistake in the Krasnodar defence gave Johansen the opportunity to net from a tight angle.
Deila changed his entire line-up for the second half and was rewarded as young striker McGregor slotted Celtic's final goal five minutes after the restart.
New boss Deila is readying his men in central Europe ahead of their Champions League qualifier against KR Reykjavik in Iceland on July 15.