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Broad was ruled out of the remainder of England's tour with an abdominal injury earlier this week, leaving the door open for Woakes to join Craig Kieswetter, Luke Wright, Michael Yardy and James Tredwell in the 17-man squad named on Friday.
"We believe we've picked a well-balanced squad to cover both the two Twenty20 matches and the ensuing sevenmatch ODI series against Australia," England selector Geoff Miller said in a statement.
"This series will be the ideal lead up to the ICC World Cup, which immediately follows the tour of Australia.
"With Stuart Broad ruled out of the series weve needed to bolster our pace bowling stocks and Chris Woakes comes into the squad after knocking on the door for some time.
"Chris will be hungry for his international debut and vying for a place with a number of other quality pace bowlers."
Kieswetter would join the squad for the two T20 matches before joining the England Lions tour of the West Indies, the statement said.
Test captain Andrew Strauss will skipper the one-day team, but will not play in the Twenty20 side, which will be captained by Paul Collingwood.
The first T20 match will be played in Adelaide on January 12.
Squad:
Andrew Strauss (ODI captain, ODI squad only), Paul Collingwood (T20 Captain), James Anderson, Ian Bell, Tim Bresnan, Steven Davies, Eoin Morgan, Craig Kieswetter, (T20 squad only), Kevin Pietersen, Ajmal Shahzad, Graeme Swann, James Tredwell, Chris Tremlett, Jonathan Trott, Chris Woakes, Luke Wright, Michael Yardy
