Liverpool midfielder Allen has aggravated a troublesome shoulder problem which almost saw him miss out on Chris Coleman's original squad, while Leeds striker Morison has pulled out due to a calf injury.
Coleman responded by calling up Jermaine Easter, who is currently on loan at Millwall from their south London rivals Crystal Palace and scored in the win over Charlton on Saturday.
The boss had expected Allen to play a part in the qualifiers, despite his injury, revealing earlier this week that he had not heard anything from Liverpool manager Brendan Rodgers to suggest otherwise.
Allen requires surgery on his shoulder problem, a procedure that will sideline him for around three months, and both the player and his club are keen to have the operation soon in order to be fully fit for next season.
The 23-year-old was named in the starting line-up for Liverpool's 3-1 defeat to Southampton on Saturday, but he was withdrawn at half-time.
Coleman's men are seven points adrift of Group A pacesetters Croatia and Belgium and face an uphill battle if they are to end their long wait for a place at a major finals.