Benavides was credited with 23:10s for stopping to assist his other team-mate, Matthias Walkner, who crashed heavily 55km into the special.
“It's always a difficult day when you see someone has had a crash, and it's worse when it's your team-mate,” said the 2021 Dakar champion.
“I stayed with Matthias until help arrived and although he was in some pain, he then told me to carry on.
“I pushed hard for the rest of the stage, but it's tricky to focus after seeing something like that.
“To win the stage is amazing, and to be second overall and so close to Toby is even more of a surprise.
“With one day left all I can do is try my best and the results will be decided at the finish line.”
Walkner suffered back pain and even lost feeling in his legs during the delay in hospital treatment while another competitor was treated.
Fortunately, that was a result of the vacuum mattress he was laying in for several hours, with the Austrian cleared of any fractures.
He will, however, remain in hospital for observation.
“I‘m a little lost for words,” wrote Walkner on Instagram.
“It was a tough day. Already at the start of the competition I was unlucky. I crashed on the second day, I tried to continue and finish the race but now, on the second to last day, the Dakar is over for me.
“It took me 8 hours to get to the hospital and almost 10 hours for the MRI checks.
“Honestly, it's really scary when you start losing some feeling in your legs.
“I´m still in a lot pain but luckily nothing is broken.”
Stage 14 starts this evening (AEDT).