Liverpool midfielder Allen has suffered a recurrence of a long-standing shoulder injury that had cast doubt over his initial inclusion in Chris Coleman's party.
Leeds striker Morison has pulled out with a calf strain.
Wales have covered off the double setback by calling up striker Jermaine Easter, who is currently on loan at Millwall from Crystal Palace.
Coleman 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 that suggested he was reluctant for the player to be called up.
Allen requires surgery on his shoulder problem, a procedure which will keep him sidelined for three months, and both the player and his club are keen to go under the knife 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 was substituted at the break.
Wales are looking to build on their encouraging win over Austria last month in the qualifying double-header.
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.