Uniquify Identifiers

Brachylog, 8 bytes

{|∧ℕ₁}ᵐ≠

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Explanation

{    }ᵐ     Map on the Input:
              Input = Output…
 |            …or…
  ∧ℕ₁         …Output is in [1,+inf)
       ≠    All elements of the output must be different
            (Implicit labeling)

Java 8, 158 144 bytes

a->{int m=0;String r="",c=",",b=r;for(int x:a)b+=x+c;for(int x:a)if(r.contains(x+c)){for(;(r+b).contains(++m+c););r+=m+c;}else r+=x+c;return r;}

• .contains(m+c);m++) to .contains(++m+c);) to save 1 byte, and simultaneously converted to Java 8 to save 13 more bytes.

Explanations:

Try it here.

a->{                      // Method with integer-array parameter and String return-type
  int m=0;                //  Lowest integer
  String r="",            //  Result-String
         c=",",           //  Comma delimiter for result String
         b=r;for(int x:a)b+=x+c;
                          //  Input array as String
  for(int x:a)            //  Loop (2) over the integers in the array
    if(r.contains(x+c)){  //   If the result already contains this integer
      for(;(r+b).contains(++m+c););
                          //    Inner (3) as long as either the result-String or array-String contains the lowest integer
                          //     and raise the lowest integer before every iteration by 1
      r+=m+c;             //    Append the result with this lowest not-present integer
    }else                 //   Else:
      r+=x+c;             //    Append the result-String with the current integer
                          //  End of loop (2) (implicit / single-line body)
  return r;               //  Return the result-String
}                         // End of method

Ruby, 63 bytes

->a{r=*0..a.size;r.map{|i|[a[i]]-a[0,i]==[]?a[i]=(r-a)[1]:0};a}

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Explanation

->a{                                    # Anonymous function with one argument
    r=*0..a.size;                       # Numbers from 0 to array size
    r.map{|i|                           # For all numbers in range:
        [a[i]]                          #  Get array with just a[i]
              -a[0,i]                   #  Remove elements from array that are
                                        #    also in a[0..i-1]
                    ==[]?               #  Check if result is an empty array
                        a[i]=           #  If true, set a[i] to:
                             (r-a)      #   Remove elements from number range
                                        #     that are also in input array
                                  [1]   #   Get second element (first non-zero)
                        :0};            #  If false, no-op
                            a}          # Return modified array