The New Zealand spearhead has an irritated disc in his back, which necessitated a hospital scan last night.
He bowled five overs on the second day of the opening test against Australia at the Gabba today before walking gingerly off the field.
Wagner, a regular member of the New Zealand squad, will join the group when it reaches Perth, venue for the second test starting next Friday.
"Tim will continue to be monitored and assessed over the coming days, but it's important we have all of our bases covered," coach Mike Hesson said.
''Bringing Neil into the squad as cover assures us of that."
Wagner has played 16 tests and taken 58 wickets at 34 apiece. His most recent test was against Sri Lanka in Christchurch last December.
The 29-year-old is noted for his wholehearted bowling and solid worth ethic.
If Southee does not recover for the Perth test, Wagner will vie with Matt Henry and Doug Bracewell for most likely two seam bowling spots.
- David Leggat of the New Zealand Herald in Brisbane
