Officials tell Eyewitness News the deputy was working an extra job conducting traffic at Post Oak Boulevard and West Alabama Street when the man pulled into the intersection and stopped at around 1:45 a.m.
Police say the deputy walked up to the SUV the driver was inside and tapped on the window because the man wasn't looking at him.
"When the occupant turned, he looked at the deputy. The deputy says the occupant then pulled a weapon, a pistol, pointed it at the deputy through the window," said Houston Police Department Assistant Chief Bobby Dobbins.
Authorities say that's when the deputy grabbed his gun and fired several times.
The man in the SUV was shot in the hand. He drove off and ended up at Beechnut and the West Loop where he called 911.
He was taken to the hospital. He's expected to be OK.
No one has been charged.
The deputy was not hurt.
Follow Courtney on Facebook and Twitter.