A.J. Foyt entered the month as the polesitter's favorite after setting a fast lap of 170.875 mph in the second week of practice. However, the most dramatic story from time trials came on pole day, Saturday May 17. Rain threatened, and the qualifying session opened late. Jigger Sirois, a rookie who had drawn the first qualifying position, took to the track at 4:12 p.m. and ran three solid laps. As he approached his fourth and final qualifying lap, his pit crew — apparently dissatisfied with his pace — displayed a yellow flag and waved off the attempt. The problem: under the rules, waving off meant the attempt was voided and no further runs were permitted. Rain then returned before the next car could attempt, closing the track for the day. Sirois was left without a qualifying time. It was later calculated that his waved-off run would have been fast enough to place him 31st in the field — and depending on interpretation of the qualifying rules, might even have won him the provisional pole position for the entire week.
Rain washed out the second day of time trials, making it the first time in modern history that the entire first weekend of time trials was lost to weather. Sirois's subsequent attempts in later rounds were also unsuccessful — he dropped a valve on a final attempt — and he never managed to qualify for the Indianapolis 500.
A.J. Foyt won the pole position on Saturday May 24 with a speed of 170.568 mph. Mario Andretti, who had crashed his primary Lotus four-wheel-drive machine in practice and suffered burns to his face, qualified the backup Brawner-Hawk for the middle of the front row. Aldo Andretti stood in for his twin brother Mario during the traditional front row photo session due to Mario's facial burns.
Andretti led the early laps before handing the lead to Foyt, who was managing the overheating tendency of his turbocharged Ford. Foyt led 66 laps in the first half before being derailed by a split manifold on lap 99, which required over 20 minutes of pit work. He returned to the race and finished eighth with a charging second half, but his title bid was finished.
Lloyd Ruby, a driver with a long history of misfortune at Indianapolis, had led after Foyt's trouble and appeared poised to finally claim his first victory. On lap 105, however, Ruby pulled away from a pit stop while the fuel hose was still attached. The hose ripped a large hole in the tank, spilling fuel and ending his race immediately.
With Ruby out, Andretti assumed the lead and was never seriously threatened again. Despite an overheating engine, a slipping clutch, low transmission fluid, and a near-brush with the wall in turn two, he maintained more than a full lap lead over second-place Dan Gurney in the closing stages. Andretti crossed the finish line nearly two laps ahead of Gurney. Andy Granatelli, who had endured years of failure at Indianapolis — first with the Novis, then with the turbine machines in 1967 and 1968 — famously planted a kiss on Andretti's cheek in victory lane.
The final 110 laps of the race ran under green flag conditions, with no yellow periods in the second half.
The 1969 race saw the last front-engined car fail to qualify, and no front-engined machine has qualified since. All 33 cars on the grid were rear-engined piston-powered machines. After the near-victories of the Granatelli Turbine in 1967 and 1968, USAC further restricted turbine entries for 1969 by reducing the annulus inlet from 15.999 square inches to 11.999 square inches. The Granatelli team abandoned the project. While turbine cars were not officially banned outright, none would ever manage to qualify again.
USAC had also begun relaxing restrictions on aerodynamic devices, permitting airfoils and spoilers as long as they were integral to the bodywork. Goodyear introduced a new wide, low-profile tire for the event.
The 1969 race was the most recent Indy 500 scheduled for a Friday. Changes to federal holiday law in 1971 moved Memorial Day to a three-day weekend format, and from 1974 onward the race has consistently been held on a Sunday.