The 46-year-old "30 Rock" star came onstage to hand out the outstanding drama award and was welcomed with a standing ovation, said The Hollywood Reporter.
The disastrous highway accident in June 2014 left him severely injured and claimed the life of his friend, comedian James "Jimmy Mack" McNair.
"I miss you guys so much. Last year, Jimmy Kimmel stood on this stage and said, 'We'll see you back here next year, Tracy Morgan.' Well, Jimmy, thanks to my amazing doctors and the support of my family and my beautiful new wife.
The "Saturday Night Live" face returned to his comedy roots and cracked a joke about waking up from an eight-day coma.
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"I was just ecstatic to learn that I wasn't the one who messed up."
Later speaking to the press, Morgan termed his Emmys experience "very overwhelming."
"As the months and months went by, part of my therapy was seeing TV and seeing my friends and feeling like I'm coming back... My publicist said maybe you should let Hollywood welcome you back home. That's what happened."
"(The speech was written) by me, Lewis Kay and Jeff Stilson. We just sat down and it just came from the heart. I just wanted to say to my peers and my comrades in TV land thank you very much."
Morgan, who married Megan Wollover in August, said his recovery was more than just about getting back to comedy.
"I wanted to walk my wife down the aisle with no cane," he said.