Until the 12th amendment, there were no running mates. First place in the electoral college was President, and 2nd place was VP.
In the 1796 election (John Adams and Thomas Jefferson), the President and VP happened to be bitter enemies -- parties were forming -- and 8 years later that system was done away with.
As you point out, it is still possible it could happen, though less likely.
The House selects the President, and the Senate selects the Vice-President.