The Spaniard was neck and neck with training partner Richard Murray heading into the final 100 metres of the five-kilometre sprint.
But it was Mola who dug deepest to hold off the South African and claim the win in a time of 49 minutes and 46 seconds.
Joao Pereira completed the podium, the Portuguese collecting his first World Triathlon Series medal by outsprinting two-time world champion Alastair Brownlee, who finished fourth ahead of brother Jonathan and series leader Javier Gomez, who were fifth and sixth.
Mola had been back in the pack during the swim and on the bike, but he came to the front as part on an eight-man group, which included Alistair Brownlee and Gomez, at the start of the run.
Alistair Brownlee and Gomez then formed a group that tried to break from the field.
Murray was the first to claw back the leaders, but it was Mola who executed his gameplan to perfection, and in doing so became the first man outside of Alistair Brownlee or Gomez to win a World Triathlon Series race in London.
For Gomez, his sixth-placed finish sees the best winning run in the Series’ history come to an end, but he still maintains the lead at the top of the rankings.
In the women’s race, Gwen Jorgensen headed an American one-two ahead of Sarah Groff, and now moves ahead of Britain’s Jodie Stimpson in the overall rankings.
Jorgensen finished 28 seconds ahead of her compatriot in a dominant display, which comes just two weeks after her win in Yokohama, while she also erased painful memories of 2013 where a crash on the bike at the same venue ended her hopes of claiming the World Championship title.
Australia’s Emma Jackson was third, while Stimpson finished a disappointing 11th.
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