Watson was named in the first Test squad in November but was forced to withdraw when he tore his hamstring in a domestic one-day game.
His place was taken in the first Test by Michael Clarke, who has scored enough runs to cement his place for the remainder of the summer.
When Damien Martyn retired after the second Test Watson was still out injured and the selectors opted for Andrew Symonds.
Symonds now has the chance to nail down his spot, leaving Watson on the outer once again.
Watson was in good form when he broke down Saturday.
He bowled Mark Cosgrove off an inside edge in his first over of the morning then bowled Callum Ferguson with the second ball after lunch.
He pulled up sore after sending down a bouncer to Jason Gillespie and soon left the field.
Queensland coach Terry Oliver said it appeared the strain was in a slightly different area of the same hamstring.