RHS first and then LHS. And at any side, the evaluation order is left to right.

a[-1] += a.pop() is same as, a[-1] = a[-1] + a.pop()

a = [1,2,3]
a[-1] = a[-1] + a.pop() # a = [1, 6]

See how the behavior changes when we change the order of the operations at RHS,

a = [1,2,3]
a[-1] = a.pop() + a[-1] # a = [1, 5]

The key insight is that a[-1] += a.pop() is syntactic sugar for a[-1] = a[-1] + a.pop(). This holds true because += is being applied to an immutable object (an int here) rather than a mutable object (relevant question here).

The right hand side (RHS) is evaluated first. On the RHS: equivalent syntax is a[-1] + a.pop(). First, a[-1] gets the last value 3. Second, a.pop() returns 3. 3 + 3 is 6.

On the Left hand side (LHS), a is now [1,2] due to the in-place mutation already applied by list.pop() and so the value of a[-1] is changed from 2 to 6.

Let's have a look at the output of dis.dis for a[-1] += a.pop()¹⁾:

3    15 LOAD_FAST            0 (a)                             # a,
     18 LOAD_CONST           5 (-1)                            # a, -1
     21 DUP_TOP_TWO                                            # a, -1, a, -1
     22 BINARY_SUBSCR                                          # a, -1, 3
     23 LOAD_FAST            0 (a)                             # a, -1, 3, a
     26 LOAD_ATTR            0 (pop)                           # a, -1, 3, a.pop
     29 CALL_FUNCTION        0 (0 positional, 0 keyword pair)  # a, -1, 3, 3
     32 INPLACE_ADD                                            # a, -1, 6
     33 ROT_THREE                                              # 6, a, -1
     34 STORE_SUBSCR                                           # (empty)

The meaning of the different instructions is listed here.

First, LOAD_FAST and LOAD_CONST load a and -1 onto the stack, and DUP_TOP_TWO duplicates the two, before BINARY_SUBSCR gets the subscript value, resulting in a, -1, 3 on the stack. It then loads a again, and LOAD_ATTR loads the pop function, which is called with no arguments by CALL_FUNCTION. The stack is now a, -1, 3, 3, and INPLACE_ADD adds the top two values. Finally, ROT_THREE rotates the stack to 6, a, -1 to match the order expected by STORE_SUBSCR and the value is stored.

So, in short, the current value of a[-1] is evaluated before calling a.pop() and the result of the addition is then stored back to the new a[-1], irrespective of its current value.

¹⁾ This is the disassembly for Python 3, slightly compressed to better fit on the page, with an added column showing the stack after # ...; for Python 2 it looks a bit different, but similar.