Five-times Sprint Cup champion Johnson led through the last 10 laps to finish ahead of Dale Earnhardt Jr and Mark Martin.
Patrick, who was the first woman to start on pole in the 500, went into the final lap in third place but fell back five places during the final push to the finish line.
Johnson won the race in 2006 but had not finished above 27th in the last six editions of stock car racing's premier event.
The race came a day after a crash in the second tier Nationwide race at the Daytona International Speedway left 28 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 with nine cars involved, several spinning off the track including one of the favorites Tony Stewart and 2007 Daytona 500 winner Kevin Harvick.