The 23-year-old needed 6,200 points for Olympic qualification and achieved it with ease in Austria.
World silver medallist Brianne Theisen-Eaton defended her title, setting a world-leading 6,765-points total.
Latvia's Laura Ikauniece-Admidina was second, with Germany's Carolin Schafer third.
Johnson-Thompson, the 2014 champion, was second overall after setting three personal bests on a promising opening day, but fell behind on day two after failing to shine in the long jump and javelin.
The Liverpudlian recorded two legal jumps in the long jump, the furthest of which was 6.17m - the sixth best of the field and some distance below her lifetime best of 6.92m.
But while her performance in one of her favoured events diminished her chances of challenging reigning champion Theisen-Eaton for the title, it was enough to keep her on course for Olympic qualification - and a step towards eradicating the demons of last year's World Championships in Beijing.
It was the long jump, her disastrous three fouls, which ruined her chances of winning a medal last summer and the Briton had admitted she would be nervous on the runway in Austria.
When asked whether she was worried about the long jump in Rio, she replied: "Yeah, I'm not going to lie, there will be but I know I can get through it. It's just about getting my confidence back.
"I know that I have a big jump in me. The shot put is definitely a bigger concern for me."
This was her first major competition after undergoing a knee operation last autumn and she had repeatedly stated her main aim was to obtain the points needed for Rio, where she is expected to vie for gold with reigning Olympic champion Jessica Ennis-Hill and Theisen-Eaton.
Needing 35m or more to keep her on course for Rio, Johnson-Thompson threw 36.66m in the javelin - the second worst in the field - which left her requiring a time of 2:24.50 or better in the 800m.
With a personal best over two laps of 2:07.64 there was little to worry about, although the strapping on her left leg perhaps explained why she took it easy in the race, clocking 2:16.81 for the 11th quickest time overall.
"I didn't want to push and injure myself so I just took it as an easy day. The feeling is one of relief more than anything else," she said.
"My goal is definitely a gold medal still in Rio. I've got a lot to work on between now and then but this is my first time back after surgery, so I know exactly what I need to work on."
British teenager Morgan Lake withdrew from the competition after a disappointing opening day in Austria which left her 29th overall and unlikely to achieve the total needed for Rio.
Her coach and father, Eldon Lake, revealed the 19-year-old had been suffering with an adductor injury, missing a number of weeks of training leading up to the competition.
"It was always a gamble trying to compete while managing an injury and, on this occasion, it didn't pay off," he told BBC Sport.
Lake, who will have other opportunities to qualify for Rio, said on Twitter: "Disappointed doesn't come close to how I feel right now, but it has made me even more determined to get the qualifying score and fight for my place in Rio."
The 6,200-points total is more than was needed for London 2012, while attaining that mark would require Lake to break her personal best of 6,148, set in Eugene in 2014 when she became world junior champion.
In the decathlon, Britain's Ashley Bryant fell 44 points short of the Olympic qualifying standard of 8100.
The 25-year-old, who had to borrow vaulting poles after Swiss Air had lost them, could only clear 4.40m - 30cm below his personal best.
Compatriot John Lane, competing for the first time since injury, withdrew after the first day as his poles also failed to arrive.
He tweeted: "Some things are manageable... trying to pole vault in Austria when your poles are in Birmingham is not. Cheers @FlySWISS."
Heptathlete Katarina Johnson-Thompson qualified for the Rio Olympics, finishing with 6,304 points in coming sixth at the Hypo-Meeting in Gotzis.