The 130-year-old trees were dying despite two years of efforts to reverse the effects of a potent herbicide poured onto the soil in 2010, CNN reported.
For decades, students had covered the trees in Toomer's Corner with toilet paper to celebrate an Auburn win.
Saturday night, Auburn students and fans rolled the trees one last time.
Harvey Updyke, a fan of rival University of Alabama, poisoned the oaks after the Crimson Tide lost to Auburn in November 2010. He anonymously confessed two months later on a radio talk show.
Updyke, who is in his mid-60's, was arrested and pleaded guilty in March to criminal damage to an agricultural facility. He will serve at least three months of a three-year sentence and be under five years of supervised probation.
Updyke must observe a 7 p.m. curfew and is banned from attending any collegiate event and from entering Auburn property.