Thomas has been called up from a holiday resort in Cyprus to be thrust straight into Test match action against the World Champions for the second and final match of the tour in just six days time.
"We are fortunate in that Rhys knows this squad well, it's a great chance for him and he will take little time to settle in," said Forwards Coach Robin McBryde.
"With only two hookers on the tour with us, he will definitely play a part for us on Saturday which won't be easy for him after joining us so late, but we have confidence in him."
Llanelli Scarlets hooker Rees sustained a tear to his calf muscle and will now be several weeks in rehabilitation.
"It's a big disappointment for Matthew especially as he has become such a major influence on the team. He is very sad to be missing out on the second Test but we know he'll be putting a tremendous effort in to be back on the field as soon as possible."
Thomas Rhys THOMAS (CARDIFF BLUES - Cap No 1,035)
DoB: 23.04.82. 6'0" / 1.83m. 16st 8lbs / 105kgs
International record: 26 caps (W 10, L 15, D 1; 5 pts - 1T)