According to the script,
Starting on Page 51:
The Pilot’s legs are on fire.
PILOT Meine beine! Meine beine! Hilf mir! Hilf mir!
PILOT My legs! My legs! Help me! Help me!
EXT. REAR FRENCH FARMHOUSE - CONTINUOUS
Schofield and Blake drag the pilot by his shoulders - the true extent
of his injuries laid bare in the daylight. The flames have done bad
damage. His trousers have been partially burnt off, blood streaks down
his legs. The Pilot’s blue eyes dart at them, in agony. He shivers
violently with shock, his lips form words, his voice is a harsh
whisper.
(N.B. None of the German dialogue will be subtitled. We should
understand only what Blake and Schofield understand.)
PILOT Lazarett, Kamerad. Bitte. Bitte. Wasser. Wasser.
PILOT Military hospital, comrade. Please. Please. Water. Water.
They look down at the Pilot, shocked, unsure of what to do. Schofield
turns to Blake.
SCHOFIELD (sotto to Blake) We should put him out of his misery.
Schofield and Blake share a look.
BLAKE No. Get him some water. He needs water.
Blake kneels beside the pilot, gently cradles his head on his knees.
The pilot struggles, terrified and in pain.
Then continued on Page 52.
Schofield moves to the water pump, his back to Blake and the Pilot.
BLAKE (O.S.) (CONT'D) It’s alright, you’re alright. Stay still. Stay
still...
PILOT Bitte töte mich nicht. Ich möchte leben.
PILOT Please help me, I don’t want to die.
I will point out the N.B. at the top. It was Sam Mendes' intention to NOT provide sub-titles. The viewers were only supposed to understand what the two protagonists understood (which of course, only works if you, as a viewer, don't understand German and DO understand English.)
There is just a slight bit more, but as it is a major plot point, I am ending here.
There are usually many inconsistencies between an initial script and what we actually see (and hear) in the final screened version, but in this case, since the author of the script and the director are the same person, I place more trust in that this is fairly accurate to the final movie.
NOTE: Regardless of Mendes' intention of the viewers not knowing what the German pilot was saying (because the protagonists didn't either), as has been pointed out by @HorusKol in a comment, the translation (in the script) of the line:
PILOT Bitte töte mich nicht. Ich möchte leben.
isn't (or shouldn't be):
PILOT Please help me, I don’t want to die.
but rather:
PILOT Please do not kill me, I want to live.