The Oxford and Cambridge boats were side by side after 10 minutes and 30 seconds when the sight of a man in the river forced them to stop.
It was decided the two boats would return to Chiswick Bridge to restart.
Cambridge went on to win with ease after Oxford broke an oar in a clash moments after the resumption.
Oxford bow man Alex Woods collapsed in the boat after they crossed the line and he was transferred to the race launch for medical treatment, with the traditional post-race presentation ceremony abandoned.
A closely-fought race had looked to be heading for an exciting finish going into the final bend, only for a man wearing a black wetsuit to swim in front of the boats and narrowly avoid being hit by the oars of the Oxford crew.
Race umpire John Garrett said: “It was totally unbelievable. We are grateful to Matthew [Pinsent] for spotting the swimmer. We thought it was some debris then we realised it was a swimmer.
“I wasn’t sure if he was going to get out of the way in time, it was quite clear he was waiting for the boats to come across him, so I just had to stop the race.”
Reserve umpire Matthew Pinsent added: “It’s not ideal but given those circumstances what could we do? It’s a safety issue. Fortunately we spotted him and stopped the race. We couldn’t possibly have carried on.”
The last time the race had to be restarted was in 2001 when there was a clash of blades.
The two boats headed back to the halfway point and the race restarted after a 31-minute delay, but Oxford’s Dr. Hanno Wienhausen broke his oar in a clash with Cambridge and the contest was effectively over as eight men took on seven.
Oxford had gone into the race as the defending champions, but Cambridge’s victory extended their lead overall in the contest to 81-76.
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