Five-times Sprint Cup champion Johnson led for the final 10 laps to finish ahead of Dale Earnhardt Jr and 54-year-old Mark Martin.
Patrick, who was the first woman to start on pole in the 500, went into the final lap in third but fell back five places during the final push to the finish line.
Driving the number 48 Chevrolet for Hendrick Motorsports, Johnson first won the race in 2006 but had not finished above 27th in the last six editions of stock car racing's premier event.
"I had a lot of confidence in those final two laps leading the train because I knew just how fast this car was," said Johnson.
The race came a day after a crash in the second tier Nationwide race at the Daytona International Speedway left around 30 fans needing treatment after debris flew into the crowd.
As usual there were some wrecks in the always incident filled race with an early collision on lap 33 involving nine cars but there were no injuries.
Several vehicles span off the track, including favorites Tony Stewart and Kasey Kahne, and previous Daytona winners Kevin Harvick and Jamie McMurray.
It was more disappointment for Stewart, who having won virtually every honor in the sport has yet to taste success in the famous Daytona Victory Lane.
Stewart took little comfort from the fact there is a long season ahead.
"To hell with the season. I wanted to win the Daytona 500," he said. "We had a car that we could pass with today. We were passing cars by ourselves.
"I don't know what started it, but we just got caught up in another wreck," added Stewart.
Patrick conceded her inexperience may have cost her at the decisive stage of the race but that her performance was more significant than winning pole position.
"I think it was better to have run up in the top 10 all day ... being able to stay up and lead at one point for me that was more of an accomplishment", she said.
But Johnson proved too quick for Patrick and the pack.
"Once Jimmie got into the outside line he showed that he was fast. It was a steady day for me. Nothing super-duper eventful," she said.
The 30-year-old former Indy Car driver led for five laps shortly before the halfway stage, becoming the first woman drive to lead the Daytona 500. She had lost her pole position to Jeff Gordon on the first lap.
Earnhardt Jr, whose father died at in the race 12 years ago, finished second in the Daytona 500 for the third time in four years.
Johnson powered past reigning Sprint Cup champion Brad Keselowski, who finished fourth, after the final re-start with his challengers unable to match his speed.
After a restart on the 182nd lap following the fifth caution of the race Keselowski and Johnson jousted for the lead while their rivals closed the gap.
Debris forced another caution, setting up a six-lap sprint to the flag with Johnson in the lead in the outside lane and he did not give an inch.
The victory was the 61st of Johnson's career in his 400th start in the NASCAR Sprint Cup Series.
"It was just awesome, there is no other way to describe it," said Johnson.
"I felt like I was sitting on something all day and was just ready to have some fun when it counted - and I did," he said.
(Editing by Gene Cherry/Peter Rutherford)