Hairston hit leadoff on Tuesday and started at second base, allowing David Eckstein, who was activated from the 15-day disabled list because of a calf injury over the weekend, to have the day off.
Hairston, who said he had never had migraines in his life before last week, started feeling the headaches during the Padres' four-game series in Chicago last week, but the pain got much worse in Milwaukee.
"It hit me hard [in Milwaukee]," Hairston said. "You want to poke holes in your head to get rid of the pressure ... I was a mess."
Hairston said he could have played Sunday after taking medication throughout the weekend, but the Padres decided to play it safe and give him an additional day to get well.
The improved health of Hairston, combined with the return of Eckstein and the acquisition of Miguel Tejada, may finally allow Hairston to fill the utility player role that the Padres always thought he would when they signed him in the offseason.
Injuries to Everth Cabrera and Eckstein forced the Padres to make Hairston the everyday shortstop or second baseman at various times this season, but now Hairston will likely be able to seamlessly transition between second, third and shortstop for the remainder of the season to spell Eckstein, Tejada and Chase Headley on certain days.
"That's a good thing -- his versatility, his flexibility," Padres manager Bud Black said. "That's how we envisioned it, but you never know what's going to happen during the course of the season. He's proven to be a very valuable part of our club, but there's no doubt that he gives us the flexibility to move him around the diamond and we don't lose a thing."
Hairston is batting .252 this season with 10 home runs, 49 RBIs and 51 runs scored.