The Spaniard, who broke his left tibia and fibula less than a month ago, halted the session with eleven minutes remaining after a highside at the final turn.
Barbera had clipped the kerb as he made the right/left change of direction that leads onto the home straight - causing the rear of his Pramac Ducati to swing around and fling Barbera over the front.
Slow to get up, an ambulance was sent to take the Spaniard to the medical centre, where he complained of chest rather than leg pain. Toni Elias
is on standby should Barbera be unable to continue.
Crutchlow's team-mate Andrea Dovizioso
was ranked behind Barbera in eleventh, with Avintia's Yonny Hernandez the leading CRT ride in twelfth place, 2.4s from Stoner.
Team-mate Ivan Silva also lapped quicker than the slowest manufacturer rider, Karel Abraham (Cardion AB).
Colin Edwards was 19th for Forward Racing, which is continuing with the Suter-BMW this weekend.
Two home wild-card CRT entries are present at Indy: Steve Rapp (Attack Performance), who took part in the previous Laguna Seca round but failed to qualify, plus fellow AMA veteran Aaron Yates, who is making his MotoGP debut for GPTech.
Rapp was 20th (+4.694s) and Yates, whose Suzuki-powered bike is painted in a Rizla-style light blue, 23rd and last (+6.129s). Both have recently tested at Indy.
Second practice will take place this afternoon.
No rider has yet won twice at Indianapolis, with Rossi, Lorenzo, Pedrosa and Stoner the former event winners.
Friday practice (1):
1. Casey Stoner
2. Dani Pedrosa
3. Nicky Hayden
4. Ben Spies
5. Stefan Bradl
6. Alvaro Bautista
7. Cal Crutchlow
8. Jorge Lorenzo
9. Valentino Rossi
10. Hector Barbera
11. Andrea Dovizioso
12. Yonny Hernandez
13. Aleix Espargaro
14. Karel Abraham
15. Mattia Pasini
16. Randy De Puniet
17. Ivan Silva
18. Michele Pirro
19. Colin Edwards
20. Steve Rapp
21. Danilo Petrucci
22. James Ellison
23. Aaron Yates