The veteran beat the benchmark set by the reigning champion - who spent most of the session on provisional pole - with his second lap of 52.799 seconds, just edging his team-mate by two thousandths of a second.
Chevrolet dominated qualifying, taking seven out of the top 10 spots on the grid. Hendrick Motorsports placed all of its cars in the top-six starting spots, with all of them dipping under the 53 second mark.
Earlier this year Hendrick also swept the front row at Talladega and eventually the outfit had its drivers contending for victory on the final lap, Johnson claiming his first win of the season.
The Wood Brothers Ford of Daytona 500 winner Trevor Bayne was able to split the Chevy's at the front with the fourth fastest time - the best of those having to qualify on speed - while Roush Fenway cars filled the remaining spots in the top nine, David Ragan taking eighth ahead of Chase leader Carl Edwards.
Kurt Busch was the best among the Dodges on the grid in 14th, while Toyota teams struggled for speed on their own despite looking quick while drafting in tandem during practice. JTG Daugherty's Bobby Labonte was the fastest in 21st.
Geoffrey Bodine, Scott Speed, TJ Bell and Josh Wise failed to make the field.
Pos Driver Team/Car Time Gap 1. Mark Martin Hendrick Chevrolet 52.799s 2. Jimmie Johnson Hendrick Chevrolet 52.801s + 0.002s 3. Clint Bowyer Childress Chevrolet 52.835s + 0.036s 4. Trevor Bayne Wood Brothers Ford 52.903s + 0.104s 5. Jeff Gordon Hendrick Chevrolet 52.930s + 0.131s 6. Dale Earnhardt Jr Hendrick Chevrolet 52.934s + 0.135s 7. Paul Menard Childress Chevrolet 53.007s + 0.208s 8. David Ragan Roush Fenway Ford 53.021s + 0.222s 9. Carl Edwards Roush Fenway Ford 53.138s + 0.339s 10. Ryan Newman Stewart Haas Chevrolet 53.140s + 0.341s 11. Matt Kenseth Roush Fenway Ford 53.142s + 0.343s 12. Tony Stewart Stewart Haas Chevrolet 53.168s + 0.369s 13. Kevin Harvick Childress Chevrolet 53.186s + 0.387s 14. Kurt Busch Penske Dodge 53.209s + 0.410s 15. Juan Pablo Montoya Earnhardt Ganassi Chevrolet 53.237s + 0.438s 16. Brad Keselowski Penske Dodge 53.250s + 0.451s 17. Travis Kvapil Front Row Ford 53.250s + 0.451s 18. Greg Biffle Roush Fenway Ford 53.264s + 0.465s 19. Marcos Ambrose Petty Ford 53.278s + 0.479s 20. Kevin Conway NEMCO Toyota 53.291s + 0.492s 21. Bobby Labonte JTG Daugherty Toyota 53.297s + 0.498s 22. Regan Smith Furniture Row Chevrolet 53.305s + 0.506s 23. Michael Waltrip Waltrip Toyota 53.310s + 0.511s 24. AJ Allmendinger Petty Ford 53.318s + 0.519s 25. Jeff Burton Childress Chevrolet 53.318s + 0.519s 26. Kasey Kahne Red Bull Toyota 53.326s + 0.527s 27. Joe Nemechek NEMCO Toyota 53.372s + 0.573s 28. JJ Yeley Front Row Ford 53.393s + 0.594s 29. Michael McDowell HP Toyota 53.394s + 0.595s 30. Brian Vickers Red Bull Toyota 53.481s + 0.682s 31. Denny Hamlin Gibbs Toyota 53.514s + 0.715s 32. Terry Labonte FAS Lane Ford 53.528s + 0.729s 33. Andy Lally TRG Ford 53.532s + 0.733s 34. Kyle Busch Gibbs Toyota 53.563s + 0.764s 35. Joey Logano Gibbs Toyota 53.565s + 0.766s 36. David Reutimann Waltrip Toyota 53.595s + 0.796s 37. Martin Truex Jr Waltrip Toyota 53.596s + 0.797s 38. Landon Cassill Phoenix Chevrolet 53.616s + 0.817s 39. Jamie McMurray Earnhardt Ganassi Chevrolet 53.641s + 0.842s 40. David Gilliland Front Row Ford 53.669s + 0.870s 41. Dave Blaney Baldwin Chevrolet 53.696s + 0.897s 42. Casey Mears Germain Toyota 54.262s + 1.463s 43. Robby Gordon Gordon Dodge 54.627s + 1.828s Did not qualify: Geoffrey Bodine Baldwin Chevrolet 53.637s + 0.838s Scott Speed Whitney Ford 53.956s + 1.157s T.J. Bell LTD Powersports 54.080s + 1.281s Josh Wise Max Q Ford 54.085s + 1.286s
