The Glasgow centre suffered the injury during the Scots' 27-3 defeat to South Africa at Murrayfield on August 25, and has been slow to respond to treatment since.
He will not play against the Portuguese this weekend, but Scotland coach Frank Hadden hopes to have the 27-year-old back available for selection for the remaining Pool C games.
"Andy Henderson is unavailable to play against Portugal," said Hadden.
"He has a dead leg, and he had to have some blood removed at the beginning of the week.
"But he will be fine for the following week."
A spokesman for the Scotland squad added: "Andy suffered deep bruising in the match against South Africa and he has been slow to respond to treatment.
"He is doing conditioning work with the physio and will take part in individual training."
Scotland have no other injury concerns ahead of the Portugal match.
Henderson - a first choice in midfield under Hadden - has been in good form in the World Cup warm-up matches, scoring a hat-trick of tries in the 31-21 win over Ireland on August 11.