Alternation and Zayat Stables' Prayer for Relief, both 4-year-olds, dueled for much of the 1 1/8 miles. Prayer for Relief briefly had a half-length lead at the three-quarter call, but Alternation fought back to narrow lead on the far turn.
Alternation, ridden by Luis Quinonez, was in front by a head in mid-stretch, and at the wire, the margin of victory was a nose over Prayer for Relief and Mark Guidry.
Fractions for the Governor's Cup, run on a fast track, were :24.13, :48.17, 1:12.87, and 1:37.20. The final time was 1:49.27.
Alternation, by Distorted Humor , won his fifth stakes of the year from six attempts for trainer Donnie Von Hemel.
"I thought it was a tremendous effort tonight," Von Hemel said. "We gave six pounds to (Prayer for Relief). It was a big effort by both horses. To go the last eighth of a mile in 12 seconds flat, that's racehorse right there."
Homebred Alternation, who paid $3.20 and $2.10 as the favorite in the five-horse field, earned $120,000 for the Governor's Cup victory and now has $1,032,727 in earnings. Prayer for Relief was worth $2.20. There was no show wagering. Get in Da House finished 6 1/4 lengths back in third, followed by Dreaminofthewin and Stachys.