The 31-year-old, who won in 2014 and 2016, finished third in his heat in 46.27 seconds at the Olympic Stadium in Berlin.
Rooney came fifth at the British trials last month, but as defending champion he had the right to compete if deemed fit enough.
He said: "Job done, only just about. It was a poor second half of the race, the first half was the best I've run all year.
"I was just way too relaxed running off the bend, I thought I was at 44-second pace because it's the best I've felt all year. I then sort of stopped and was trying to stride off the bend.
"I should have been more professional, more assertive with the race and tried to dominate it. My bad. I'll get a tough semi-final, but I'm just going to have to spank it."
Dwayne Cowan survived a yellow card after his first start to win his heat and progress to Wednesday's semi-finals in 45.75secs.
Lynsey Sharp, Adelle Tracey and Shelayna Oskan-Clarke all reached the 800m semi-finals.
Sharp said: "I've been climbing the walls just waiting to get out, it's been a boring couple of days and I needed to get out and compete. I felt so much more like myself out there and I was getting excited as I ran around feeling like me again."
In the decathlon, France's world champion Kevin Mayer produced three no jumps in the long jump and then opted not to throw in the shot put, opening up an easier route to the podium for British hope Tim Duckworth, who won the long jump.
The main Tuesday focus is on the 100m with Zharnel Hughes, Reece Prescod and CJ Ujah competing for the men's title in the evening.
Hughes is narrow favourite ahead of France's Jimmy Vicaut, with Prescod, the only Brit to reach the World Championship final last year, third.
Dina Asher-Smith, Imani lansiquot and Daryll Neita are bidding to reach their 100m final, with Asher-Smith starting her treble bid ahead of the 200m and 4x100m relay.
