ACR MLG ALT DEV OVERSHOT DURING SID FROM EWR THAT WAS GIVEN IN VISUAL FORM VIA ACARS.

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AFTER TKOF FROM NEWARK; DEP ROGERED OUR INITIAL CALL 'CLBING TO 5000 MSL'. WE WERE IN A DEP TURN TO 220 DEG HDG; CLBING THROUGH 4200 MSL FOR 5000 MSL WHEN THE CTLR SAID; '...LEVEL OFF AT 4000'. I QUICKLY ARRESTED THE CLB AT 4400 AND DSNDED TO 4000 MSL. (THE REMAINDER OF THE FLT WAS ROUTINE.) IN REVIEWING THE PREVIOUS EVENTS I WAS SHOCKED TO FIND THAT OUR INITIAL ASSIGNED ALT WAS MODIFIED VIA ACARS TO 2500 MSL (PUBLISHED 'EWR 3 DEP' FROM RWY 22 ALT IS 5000 MSL). I HAD READ THE ACARS CLRNC AT THE GATE; SET THE ALT ALERTER; BRIEFED IT DURING THE 'BEFORE TKOF CHKLIST'; BUT SOMEHOW MISSED SEEING THE LAST LINE AT THE BOTTOM OF THE ACARS SCREEN '...EXCEPT MAINTAIN 2500'. MY FO AND I WERE BOTH CAREFUL TO SET THE ALT ALERTER; XCHK AND CALL OUT ALL ASSIGNED ALTS DURING THE DAY. IN RETROSPECT; FATIGUE MUST HAVE PLAYED A PART IN THIS OCCURRENCE. PRIOR TO OUR EWR BLOCKOUT; THIS WAS OUR FIFTH OF 5 SCHEDULED LEGS; ALL IN THE NE CORRIDOR; HAVING FLOWN 6:06 BLOCK HRS AND 13:10 HRS ON DUTY. SUPPLEMENTAL INFO FROM ACN 185409: WE DEPARTED EWR 20 MINS LATE. I CALLED OUT OF APPROX 1000 FT CLBING TO 5000 FT. IN THE BACK OF MY MIND I FELT ODD ABOUT THE ALT; HOWEVER; 5000 FT WAS SET IN THE ALT ALERTER AND THE CTLR ROGERED MY READBACK; ALLAYING MY FEARS. MY SUSPICIONS WERE CONFIRMED WHEN I SAW THAT OUR EWR 3 DEP WAS MODIFIED WITH A 2500 FT ALT RESTRICTION INSTEAD OF THE PUBLISHED 5000 FT. I HAD INITIALLY SET 2500 FT IN THE ALT ALERTER ON THE GND. THE CAPT HAD NOT NOTICED THE ALT CHANGE FROM THE PUBLISHED DEP AND SET IT TO 5000 FT AS PUBLISHED.