GolfScript, 85 bytes

{(;);}:r;", "%(r\(r n+:c;;.,\'|'%.,@\-)):l;0:m;{.,0>}{" "m*\(.,m+:m l\-" "\*+c@}while

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GolfScript, 85 bytes

{(;);}:r;", "%(r\(r n+:c;;.,\'|'%.,@\-)):l;0:m;{.,0>}{" "m*\(.,m+:m l\-" "\*+c@}while

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#2017 Update - GolfScript - 71 bytes

', '/~~:c;~1/.,\.{'|'=},,@\-):l;['|']/0:i;{.,i+:i l i-' '*c+\' '*"
"\}/

###Explanation

', '/~~:c;~1/        # Parses input
.,\.{'|'=},,@\-):l;  # Computes string length without '|'
['|']/               # Splits the array
0:i;                 # Counter
{.,                  # Length of the substring
i+:i                 # Counter update
l i-' '*c+\          # Adds spaces after the substring 
' '*"\n"\            # Adds spaces before the next substring
}/                   # ...For each substring