Looking into it, in theory, Chocobo could win by retreating & planning cleverly.
Victory Conditions: Killing the opponent, removing the opponent from the battlefield for at least one week (
BFR), knocking the opponent out for at least one hour, or incapacitating the opponent by putting him in a state in which he can not harm the other fighter(s) for over a day, are to be assumed as victory conditions.
If Sonic can't get to Chocobo for over a day, that would fulfill a win condition, I believe?
First off, looking at the profile's Powers & Abilities & how it cites ALL of Chocobo's Jobs/Classes, saying
"Possesses a wide of variety of techniques from the following jobs:" (And then it lists all the classes.)
Two good opening moves are actually the Scholar Class's basic skill & the White Mage's ultimate:
Gauge (The in-game description of which is
"Learn everything about one foe.".) &
Raise.
If Gauge told Chocobo about Sonic's Time Manipulation, that'd be great, but even without that, I doubt it's Sonic's first resort; AFAIK, he doesn't use Chaos Emeralds on basic enemies, & even against bosses, he usually uses them for the statistics amp; I dunno of many fights where Sonic in base uses Time Stop right away or even often. He COULD, but it's unlikely.
Using Escape (In-game, random within Dungeon Floor.) or Teleport (In-game, out of the Dungeon entirely.), Chocobo could teleport away from Sonic, & Sonic may not know where Chocobo went even if he did have a Chaos Emerald (In Sonic's base, CE are only "sometimes" equipment, apparently.)
Failing that, Chocobo can use the Brooch of Memories to go into the dreams of a sleeping being (Surely there's other life in New York's Central Park; Or, Chocobo could try unleashing a devastating/distracting
Magicite summo , put the summon to sleep, then go into the summon's dreams.), putting something other than Sonic (Immunity Idol, which Chocobo might know about because Gauge.).
Sonic's only Dimensional Travel feats are going back to his home dimension, & his teleportation in bas is only hundreds of meters, & I doubt he's used it well on someone unwilling he doesn't know the location of, & speed is equalized.
Pursuit could be difficult, since Sonic would have to find wherever "outside the Dungeon" is (Outside the battle location, I assume; For use of Teleport.) or find a specific some person or monster at random who's asleep.
Or if it was a summon, he loses the chance to pursue the moment the summon leaves/despawns with Chocobo in the dream of the summon, since Chocobo may be in the dream of a being in another universe, & Sonic hasn't show Dimensional Travel except to his own home world.
From there, Chocobo can leave the dreams/memories by completing the dungeon inside -which also tend to contain supplies, with or without enemies, like Potions, Ethers, Gysahl Greens (food), etc.- & even have safety.
So even if Sonic DID get into the dream of a Summon or whatever, Chocobo could be revived through Raise if killed, then Teleport, set up Raise, & repeat.
Even if Sonic takes less than 24 hours chasing down Chocobo, it still has time to set up Speed & other buffs on itself, use Scholar's Search or Thief's Alert to be able to track anything in whatever area it is in, & prepare an ambush, either through buffed movement, unleashing Summons when Sonic arrives, or even trying to rob Sonic of his Chaos Emerald, Immunity Idol, or other equipment, given Chocobo has mastered several Thief skills, robbing Sonic.
TL;DR - Chocobo could win by learning about Sonic via Gauge, retreating with any of several Teleportation abilities &/or Summoning, then waiting him out for 24 hours; Sonic likely won't have a clue where Chocobo's teleport took it (One exits the current battle location, effectively, the other is random within it.) & the time bought will allow Chocobo to prepare speed & AP buffs on itself, set up tracking on Sonic, & prepare self-Resurrection. If Chocobo can get any being to hide in the Dreams of -or use a Magicite Summon that will go somewhere else after the Summon ends- that makes it even more difficult, as Sonic likely will have trouble finding it, & if he doesn't know of it, has no reason to attack a sleeping opponent he doesn't know has any relation to Chocobo.
And yes, Chaos Emerald Time Stops, but this match uses Base Sonic who only has CEs "Sometimes" & while Wisps are powerful, they're living beings. IC, I'd assume Sonic would hesitate to kill Wisps for a fight if he wasn't sure he needed to, & he may not find that out.
Ultimately, with proper planning & navigation, Chocobo can avoid Sonic for the 24 hours needed to win, & even if he does find Chocobo, it will likely have an ambush ready with several buffs, summons, self-resurrection, means of stealing Sonic's Emerald or Immunity Idol, etc. & items of its own ready.
Meaning if Sonic does give chase he could be walking into a very bad situation, as his usual IC tactics may not prepare him to being outspeed & outforced by an opponent he was just chasing.
And Sonic may not even be able to GIVE chase, as again, his Dimensional Travel has only taken him to his own world; He might not know how to get into or out of dreams.
But Chocobo can enter & exit them much easier, & as long as it can evade Sonic for 24 hours, it wins by SBA. Also, if he did get there, a stat-amped Chocobo could ambush him in such a hideout to rob him, it could steal Sonic's CE or Immunity Idol, then hit him with Sleep, Slow, Stun, Blind & such, or use his Time Stop, & still have a Resurrection of its own ready. And it could use Search or Alert to track Sonic in the Dungeon before Chocobo's in Sonic's sights to better ready the ambush.