He singled in his first at-bat and finished 1-for-4 as the Rockies beat the Giants 2-1.
"It's been a long road back," Rockies manager Walt Weiss said. "He's dealt with this a couple times in his career, and he's a guy who's had a great impact on this team, on the organization, in a few short years. He still has the passion to play, and I think there will be a smile on his face when he takes the field."
The 2014 NL batting champion, Morneau was hitting .290 with three homers and nine RBIs in 27 games before suffering the injury. He said throughout his rehab that his hope was to come back before the end of the season.
"I was honestly hoping it wasn't going to take as long as it did," Morneau said. "It was a little frustrating to go through it, but to be able to go back out there and be a part of this lineup and hopefully finish strong, it's a good day."
Morneau, 34, had concussion issues earlier in his career. While with the Minnesota Twins in 2010, he struck his head against John McDonald's knee while sliding into second base during a game against Toronto. He missed the final 78 games of that season.
Morneau also missed time in 2011 because of concussion symptoms, neck problems and a wrist injury.
The Rockies made room for Morneau on the 40-man roster by designating utility player Matt McBride for assignment.
Weiss said Morneau will not have any official restrictions, but that he would be prudent picking his spots with Morneau.
"We'll use common sense," Weiss said. "I'm not going to run him out there every day. There will be some obvious days off for him -- day game after a night game and those types of things. So it'll be built into the schedule."
The Associated Press contributed to this report.