The two teams met at Wembley last Saturday, with England winning 4-0.
The Edinburgh player is usually a wing but will replace captain Stuart Hogg at number 15 against Tonga.
Broja sustained an ankle injury in the Saints’ 2-2 draw with Burnley.
When Harry Maguire suffered a calf injury in Manchester United’s defeat to Aston Villa at the end of September it was expected he would be out of action for some time. Instead, after only one training session, he returned to face Leicester City just three weeks later and was badly at fault and set the tone in the chastening defeat by gifting his former club their opening goal. Maguire knows he was to blame.