Rooney, who broke his foot on April 29, took part in the first 20 minutes of the session at the England training base near Baden Baden.
The 20-year-old Manchester United forward then did a mixture of running, sprinting and ball work on his own with England fitness coach Ivan Carminati. Rooney will have a scan on his foot in Manchester on Wednesday.
Coach Sven-Goran Eriksson, whose side open their Group B campaign on Saturday against Paraguay, has been doggedly optimistic that Rooney can play some part in the finals.
Left back Ashley Cole, who is nursing a hamstring problem that forced him off during the first half of Saturday's 6-0 friendly win over Jamaica, also worked separately from the squad.
The FA said on Monday that Cole is expected to be fit to face Paraguay in Frankfurt.
Three players who missed Monday's final training session in England took part in their first workout in Germany - defenders Gary Neville and John Terry and captain David Beckham -- though Beckham later sat out the training match.
