The four-hour operation was performed by Dr. Robert Thompson at Barnes Jewish Hospital in St. Louis.
The 31-year-old Wells had a blocked artery in his right arm in 2006, which had to be replaced by a vein taken from his leg.
That surgery was also performed by Thompson. However, the operation Tuesday did not involve the earlier bypass in his shoulder.
Wells' condition will be re-evaluated Wednesday.
No date has been set for his return.
Wells was placed on the 15-day disabled list retroactive to April 29. He was 1-1 with a 2.29 ERA in 10 games, including one start.
Rockies pitcher Aaron Cook underwent surgery in 2004 for blood clots in his lungs and had a rib removed to relieve internal pressure.
"I think about it every day," Cook said. "I wake up and as soon as I get out of the shower, I have the scars to remind me. Same as him. He's got similar scars. It's not something that goes away; you learn to live with it. You're always thinking about it a little bit in the back of your mind."
Cook, who was on blood thinners for four months after his surgery, has been told his clots wouldn't return.
He said he plans to talk to Wells as soon as he can.
"The main thing is just getting healthy," Cook said.