The Leicester fly-half has been sidelined since damaging his ankle against Bath on May 5 and he was withdrawn from the Aviva Premiership final on Saturday with a tight groin.
But Flood looked sharp as the England touring squad were put through their attacking paces ahead of Thursday's departure for Durban.
Flood, who has not started a Test at fly-half since the World Cup game against Georgia, will compete with Owen Farrell and Charlie Hodgson for the position in England's three-Test series.
It was not all good news for England coach Stuart Lancaster, after prop Matt Stevens was ruled out of the tour with a shoulder injury suffered in Sunday's win against the Barbarians.
Stevens damaged his rotator cuff and has been replaced in the squad by Gloucester tight-head Rupert Harden, who was preparing to leave for Berlin on a friend's stag do when he received the call-up.
The 26-year-old played for the Saxons against the Irish Wolfhounds and Scotland A in January and he has established himself as the Cherry and Whites' first-choice tight-head prop this season.
Harden did not arrive at Pennyhill Park until Tuesday afternoon and his first training run finished with a gruelling session on the altitude bike to prepare him for South Africa. Stevens may not require an operation but the injury requires four weeks of rehabilitation.
Lancaster said: "It's really tough on Matt but he has been assessed by the medics and he wouldn't be able to train or play for some time.
"We wish him all the best but it's a great opportunity for Rupert, who has been the first-choice tight-head for Gloucester this season and also involved in the Saxons during the Six Nations."