South Dakota took a 48-45 edge in the third overtime on a Mason Lorber 27-yard field goal before Boyle started his team off with a 15-yard rush, then hit Hendrix three plays later for the winning touchdown.
Boyle finished with 193 yards and five touchdowns passing and 187 yards and two scores rushing for the Sycamores (5-4, 3-3 Missouri Valley Football Conference). Titus McCoy added 123 yards rushing. Hendrix had 111 yards and two touchdowns receiving.
Indiana State led 21-14 at halftime and took a 31-24 lead with 2:54 remaining in regulation on a 25-yard run by Boyle. But Austin Simmons took the Coyotes (3-6, 2-4) 81 yards in 13 plays after that, capping the drive with an 11-yard touchdown pass to Brett Samson to even it up with 16 seconds left and force overtime.
Simmons had 375 yards and three touchdowns passing for the Coyotes.
Bond, Eberle help Utah State beat San Diego St. 23-17
Dominik Eberle kick three field goals, Shaq Bond had a pick-6, and Utah State held on for a 23-17 win over San Diego State on Saturday night.
College football: Scores, Top 25 analysis, and the wild comeback you likely missed
The best of college football's latest weekend action and a recap of what the biggest Week 4 games mean for next week.
Sooners kicker charged with public intoxication
Oklahoma kicker Calum Sutherland has been arrested on a public intoxication charge.
McDonald's 4 TD passes help Hawaii beat Central Arkansas
Cole McDonald was 25-of-32 passing for 300 yards and four touchdowns and Hawaii beat Central Arkansas 35-16 on Saturday night.
Koback runs for 228 yards, 3 TDs; Toledo beat Colorado St.
Bryant Koback had 19 carries for a career-high 228 yards and accounted for four touchdowns and Toledo held on to beat Colorado State 41-35 on Saturday night.
College football Power Rankings for Week 4
See how the Top 25 shapes up after a big Week 4 for Auburn and several of its SEC rivals.