Jones missed the Boxing Day victory over Newcastle after picking up a knock in the draw at Swansea last weekend, while Rafael has not featured since the Manchester derby win earlier this month because of a hamstring strain.
Both have been making good progress with their recoveries and Sir Alex told MUTV they could both be involved at the DW Stadium.
"Phil could be ready and Rafa will be ready," said the boss. "We rested Robin [van Persie], Chicharito, Ryan [Giggs] and Paul [Scholes] against West Brom so we've got enough freshness to bring in.
"Wigan had a great result today [winning 3-0 at Aston Villa] - it'll be a hard game on Tuesday."
"Hopefully I can freshen things up again at Wigan - Phil Jones could be ready and Rafa will be ready."
- Sir Alex Ferguson