Zoom-in. Shinji is slumped down. There are lines from a nosebleed on his face.
BGM END: E-6 [ANGEL ATTACK]
KnightmareX13: After nearly being boiled alive and being knocked unconscious, all Shinji has to show for it is a nose bleed?
NemZ: I'm blaming an increase in pressure due to the heat for the nosebleed. Same thing happens when they increase the fluid pressure in ep19.
FreakyFilmFan4ever: I'm not sure what it was about the Angel that caused Shinji's current nose-bleed. Especially since his earlier incident with Rei didn't result in any of that.
EvangelionFan: Looks like the obligatory nosebleed Shinji didn't get in Episode 05 Scene 05 has finally caught up with him.
Kendrix: Shinji's Synch ratio at this point wasn't high enough for him to sustain any physical injuries yet, but his psyche was still put though considerable strain - And perhaps reacted with a nosebleed. A nosebleed is something that you can get for 'mental' reasons.