It seems pretty clear that he could have shot him (although it would have been outside of the FBI's Deadly Force Policy)
FBI special agents may use deadly force only when necessary—when the agent has a reasonable belief that the subject of such force poses an imminent danger of death or serious physical injury to the agent or another person. If feasible, a verbal warning to submit to the authority of the special agent is given prior to the use of deadly force.
Shooting someone to prevent them escaping is not permitted.
Firing shots into the air is also against policy (as it's wasteful, pointless and potentially dangerous*) but it seems clear that this act is driven entirely by frustration.
*When a bullet is fired into the air, it can stay in flight for over a minute. On the way down, it gains a velocity of between 300 and 700 feet per second—that’s more than powerful enough to kill a human. Skulls can be penetrated at a velocity of 200 feet per second.
On July 4, 1999, 9-year-old Brian Perez was hit in the head by a stray bullet. He died of his injuries the next day. At the time of Perez’s death, he was the 39th person to be killed by a stray bullet on a holiday in L.A.
Source - Newsweek
The "AAAAARGH....DAMN" outburst/scream seems to support the contention that this is driven by frustration...but the script confirms it
UTAH suddenly snaps his hand up and FIRES VERTICALLY.
HE HOWLS WITH RAGE, FRUSTRATION AND PAIN.
FIRES AGAIN. And AGAIN.
Slumping back, his shoulders slam down onto the concrete.
Straight-arming the Beretta he FIRES RAPIDLY...
Bulleting the blue sky.