To keep things simple; the Spy will be allowed both his invisibility watch and dead ringer, but no other unlockable weapons, as it is possible that Overwatch might introduce weapons in the future. I am considering all characters by their videogame depictions primarily. Also; neither character are allowed to re-enter their spawns to heal/refill. All Healthpacks are in the Overwatch format and all characters have infinite ammo. Glitches like Face-Stabbing are not allowed.
===Fight ===
Setting: 2fort
Announcer: Security alert! You must protect our intelligence.
A thud is heard just outside of the Intel Room; Sombra's Thermoptic Camo and Spy's Invis Watch are unstealthed; the two bumped into each other and fell to the floor. They see their enemy for a second before reengaging their stealth.
Sombra: Me agarraste en curva.
Spy: Oh, mon dieu…
FIGHT
Spy unstealths and fires his Revolver multiple times, hoping to hit Sombra. But he misses, as she is fully invisible.
Spy walks around, only to have something poke at his cheek.
Sombra: Boop!
Sombra has her Machine Pistol pointed directly at Spy's head.
Spy ironically smiles.
Spy: 'Oh please…'
Sombra fires anyways, and Spy drops dead.
However this is actually not the case; the Deadringer rescues the Spy and he reappears at the Sniping Post.
Sombra meanwhile has taken the Intel and is trying to leave the base, but Spy is ready.
He prepares his disguise: Widowmaker
The Spy looks in a mirror.
'Widow': Hon hon hon. I wish my Sniper looked like this…
Sombra arrives, initially spooked but friendly approaches 'Widow'.
Sombra: Oh, hey chica. Question; seen any 'queso coma monitos' around here?
'Widow': No I didn't…
Sombra walks past 'her'.
Sombra: Bueno… call a chopper and lets go.
The Spy removes his disguise, pulls out his Knife and grabs Sombra from behind. Sombra drops the intel.
Sombra: Surprise!
But Sombra deployed a Translocator a few seconds ago; just in case she fell into such a trap. She teleports away.
Spy, enraged, spits out his cigar and searches downstairs.
The two find each other and engage in a shootout. As they are indoors, they are at mid range, and some of the bullets land. Both are injured, and both flee.
Spy retreats upstairs and disguises as Reaper, but is showing pain from his wounds. He heads for a nearby Healthpack. He tries to pick up the Healthpack, but nothing happens. He scowls as he sees Sombra's skull over the Healthpack; it has been hacked.
Next to the Healthpack is a Translocator hidden behind a box. Sombra teleports to that Translocator, takes the Healthpack and looks at 'Reaper'.
Sombra: Oh wow, you don't look so good…
Spy maintains his disguise.
'Reaper': Sombra, I'm hurt. Get this Healthpack un-Hacked, now…!
Sombra: It doesn't need to be un-Hacked for you to use it. All my amigos know that.
Sombra points her gun at 'Reaper'.
Sombra: Right "Gabe?"
'Reaper': …I'm not Gabe Newell.
Sombra: Clearly not…
Sombra fires her gun, and Spy drops dead. Sombra crosses her arms.
Sombra: I know you're still here serpiente!
Sombra activates her EMP, which engulfs the entire room.
Spy is hit with the EMP, and his Deadringer is disabled.
Oh, merde.
With Spy still injured and cut off guard; Sombra is first to strike.
Sombra: Adios!
And the Spy falls; for good.
Sombra takes the intelligence and brings it to her base. The briefcase is opened; and it's pictures of Scout's mom.
Sombra: Aye… there are some secrets I didn't need to know…
===Conclusion===
Sombra's gadgets offer her significant advantages in maneuverability; allowing her to flee or ambush much more efficiently and quickly than the Spy ever could.
Sombra's Healthpack Hacks allow her to outlast Spy if their duel devolves into a war of attrition; replenishing her health at a rapid pace while giving Spy almost no opportunity to heal his wounds. Combine this with Opportunist and Sombra will have full control over the battle and can easily follow or trap the Spy; while Spy has no way to detect Sombra if she flees.
Sombra's Hack and EMP most likely would cripple Spy's gadgets as well; giving her a massive advantage since the Spy is so dependent on stealth. We cannot assume that the Spy's Sapper would impact this fight; as it cannot hack Healthpacks in TF2 and cannot hack gadgets used by other TF2 characters (like the PDF for the Engineer).
And while it is true that the Spy's Knife can instantly kill; both of these combatants are frail, lacking any superhuman endurance, and so any successful ambush at this close range has a high chance of killing anyways. Not to mention that if someone is aware of a Spy being nearby; it's only logical for them to regularly check their back.
Spy's only guaranteed advantage was his disguise kit: however it is unlikely that a deceptive genius like Sombra is going to fall for these disguises multiple times. Her Translocator is designed to escape ambushes or traps; and Sombra could in theory just Hack the Spy's disguises.