If you’ve ever heard Love Sculpture’s version of The Sabre Dance, you’ll surely agree it’s the best rock instrumental of all time. By far.
Either YYZ by Rush or Genesis The Brazilian
I’ll also nominate Genesis Second Home by the Sea. It is a separate song, although it is always performed after Home by the Sea
Is this list still not finished?
Ted Nugent’s Amboy Dukes - Hibernation
Little Feat - Day At The Dog Races
Manfred Mann’s Earth Band - Waiter, There’s A Yawn In My Ear
Grand Funk - Flight Of The Phoenix (and an extended remix if you’re into that sort of thing)
Sea Level - Storm Warning or - Midnight Pass
Gov’t Mule - Sun Dance with Chris Squire
There are probably others.
“Best”? Are we teenagers again?
Country rock instrumental.
Late Winter, Early Spring by John Denver
Maybe not “rock” rock, but howzabout Embryonic Journey - Jefferson Airplane?
If you want to bring Genesis into this I would take either of these songs instead (one long, one short, both old):
Los Endos (7:08 - live concert video - c.1976)
Horizons (1:42 - from the album Foxtrot - 1972)
“Again”? I think you mean “still”.
TDN, since you specified rock, I’m going The Call Of Ktulu (Metallica spelled it funny, I may not have spelled it their way, and I know I didn’t spell it H.P.'s way) by Metallica.
I would have voted for Water Song, and Mann’s Fate, but the zombie specified rock, that’s why I went Metallica.
I hate those. From Yngwie to Metallica to Steve, they all seem so pretentious to me, and heavy rock guitar to me never seems to blend well with orchestral arrangements. If Vai had learned his parts on violin, I’d be ecstatic. I know he can compose and read music like Zappa. I wish he was more of a multi-instrumentalist, as much as I enjoy his quirky guitar playing. But orchestral it ain’t (to me).
ETA: The beginning part is great. I kinda wish he’s let the oboes, french horns and whatnot attempt to play the whole thing without distorted guitar. It is after all a very nice melody.
Or at least afforded his volume a lesser part, upon re-watch. Still pretty neat though.
Apache is also the best music video of all time. Of all time! 
(I also vote Frankenstein)
“Maggot Brain” by Funkadelic. Eddie Hazel’s legendary, mind-melting guitar solo. Because the musicians are African-American, maybe you don’t think of this as rock. But just listen to it. This piece is definitely rock all the way, in the school of Hendrix.
Chiming in late with another vote for In Memory of Elizabeth Reed, much better piece of music than Jessica. Though maybe I like Liz Reed better because I heard it before Jessica. And another vote for Dickie Bett’s Hand Picked, also.
Pegasus from The Allman Brothers later album * Enlightened Rouges*.
The title track from Quadrophrenia is a good one, along with The Rock.
Don’t laugh but Topaz by pre-Steve Perry Journey is worth a listen. I always thought it was a Carlos Santana song, you can hear his influence through Gregg Rollie & Neal Schon.
Not quite as good is Kohoutek, but certainly worth a listen.
And speaking of Santana, not sure if anyone mentioned Incident at Neshabur upthread, kinda heavenly, angelic sounding near the end.
If God announced the world was about to be shut down and we could have just one last dance before demolition began I would ask for Sleepwalk, by Santo and Johnny.
If I may include an instrumental break in a long vocal, I would pick Traffic’s Low Spark of High Heel Boys.
Or the long version of The Doors’ Light My Fire.
Ok, this has gone on long enough. The best rock instrumental might be Jack the Ripper by Link Wray and the Raymen, but even that is really just a hair away from rocking as hard as Intoxica by the Centurians. (Seriously, that live version is singular, they are a MACHINE)
Sheesh, I’m in a surf band, trust me.
Mentioned a few times already, Rumble by Link Wray.
Why? Because it got banned because it might have turned us all into punks and no-goodniks. How’s that for a powerful instrumental!