Fighting on home turf in Aberdeen, McAllister was quickly reminded of the size of the task facing him as Shafikov dominated throughout.
And his task was further undermined by a hand injury which prompted McAllister to quit after seven rounds.
McAllister was a real underdog going into the bout but made a solid start in the opening round. However, the champion was soon asserting himself, landing with regularity and spearing the Scot with occasional power shots.
Shafikov's work was more industrious, commanding and punishing and McAllister's demeanour quickly became dispirited.
He held a clear height and reach advantage but could not keep the Russian off, instead being bullied around the squared circle and kept on the ropes.
Roared on by a partisan crowd at the Aberdeen Exhibition Centre, he shook off a lot of punishment - including an apparent hand injury - before calling it a night.
As the bell rang to restart the action the Scot got off his stool but, shaking his head, went straight to Shafikov to congratulate him on his win.
"I never seem to get a fair crack but things happen for a reason," McAllister told Sky Sports 1.