Put the index as a whole:
a[[x, y]] = a[[y, x]]
With your example:
a = np.array([[4,3,1], [5,7,0], [9,9,3], [8,2,4]])a # array([[4, 3, 1],# [5, 7, 0],# [9, 9, 3],# [8, 2, 4]])a[[0, 2]] = a[[2, 0]]a# array([[9, 9, 3],# [5, 7, 0],# [4, 3, 1],# [8, 2, 4]])