Rodrigo Palacio's last-gasp strike earned the visitors parity in Saturday's friendly at Parkhead, but Hoops boss Neil Lennon was left with more to worry about ahead of Wednesday night's Champions League third qualifying round first-leg tie at home to HJK Helsinki.
Commons, whose fine strike just before the break gave the home side the lead, hobbled off near the end leaving Celtic to finish the game with 10 men after they had used all their outfield substitutes.
Lennon had already seen striker Stokes carried off on a stretcher in the first half and that will be a concern ahead of the opening leg of their qualifier against the Finnish side in midweek.
On the plus side, the Parkhead boss will be heartened by his side's display even though Celtic go into their European campaign with only one win in six pre-season friendlies.
Lennon fielded a strong side although skipper Scott Brown was missing while right-back Mikael Lustig partnered Charlie Mulgrew at centre-back.
There was a familiar look about Stokes and Gary Hooper in the Parkhead attack.
Old foes Inter, whom Celtic had beaten in the 1967 European Cup final in Lisbon, also had well-known faces in their side such as had Matias Silvestre, Wesley Sneijder and Diego Milito.
After a minute's applause for former Celtic striker Joe McBride, who died last week, Celtic enjoyed plenty of possession and pressure in the early stages.
Mulgrew headed a Commons corner past the far post in the fourth minute.
In the 12th minute Commons' drive from 25 yards was held by Inter keeper Samir Handanovic, who made a better save at his near post from Stokes five minutes later following another Hoops corner.
Inter did little but defend and they were let off the hook again when Lustig headed a Commons corner over the bar from six yards out.
There was a scare for Lennon in the 35th minute when Stokes was carried off on a stretcher after injuring his leg blocking a Esteban Cambiasso clearance on the touchline, to be replaced by Mo Bangura.
However, there was something for the Celtic boss and the home fans to cheer five minutes from the break when his side forged ahead.
Mulgrew picked out Commons at the other side of the box with a free-kick and the Scotland international took a touch before sending a looping volley over the head of the helpless Handanovic.
Commons began the second half by cutting inside on to his left foot and firing another long-range drive just over the bar.
He forced another save from Handanovic in the 76th minute with a delightful left-footed chip that appeared to be heading towards the far corner before it was clawed away by the Slovenia keeper.
Moments later the former Derby and Nottingham Forest player injured himself stumbling over the ball and hobbled around the pitch before going up the tunnel, leaving the home side with 10 men.
Inter took advantage with moments remaining.
Celtic keeper Fraser Forster made a decent save from Cristian Chivu's 25-yard drive, then another from Milito, before substitute Palacio turned the ball in from a few yards out after a Marko Livaja cut-back.