Neben previously won the title in 2008, in Varese, Italy and at 41, she becomes the second oldest women ever to win the event after Jeannie Longo of France won aged 42 in 2001.
Neben started in the middle of the 41-rider field and had a long wait to see if her time would be beaten.
She averaged more than 47 kilometres per hour along the 28.9km course in the Qatari capital, Doha, in 38-degree heat.
“This one is more special, because of everything that happened in between,” Neben said. “I was using more energy siting there in the hot seat than out there on the bike. I feel sorry for Ellen van Dijk and at the same time I’m excited for myself."
Trixi Worrack (GER) and Annemiek van Vleuten (NED) started earlier, both setting new benchmarks. Worrack was pushed off the hot seat when van Dijk rode the second best time. The German eventually ended up sixth.
Van Dijk seemed to be on course to beat Neben’s time, when she posted the fastest intermediate times at the first two checkpoints, but she couldn’t hold on to the advantage.
At the third split, she was two seconds behind. With Neben watching nervously from the hot seat, van Dijk crossed the finish line 5.99 seconds adrift.
Van Vleuten was finally pushed from the hot seat by Garfoot, who finished in a time of 36min 45sec.
"I'm happy to be on the podium this year since I failed it by a few seconds last year," Garfoot said. "I wish it was a bit better but I’m happy to work on that for next year."
"I was fourth with 10 seconds last year. I'm third with eight seconds this year. I want first place one time before I finish my career.
"The heat didn’t impact me so much. From what I heard and saw from the juniors and under 23's, I expected the heat to play more of a role in my head.
"I was lucky I didn't struggle at all, and in the last six kilometres, I made up a lot of time there. Therefore, I think my pacing was a bit off because I was scared of the heat. I think I went out too easy but overall, I’m happy with the ride."
Russian Olga Zabelinskaya got the better of van Vleuten when she set 36min 48min 56sec, leaving the Dutchwoman in fifth place.
Last year’s silver medallist Anna van der Breggen, who won this year’s Olympic Road Race and the Individual Time Trial at the recent European Championships, finished 13th.
In the junior men’s event Brandon McNulty (USA) took gold ahead of Mikkel Bjerg (Denmark) and Ian Garrisson (USA).
Starting last from the ramp, McNulty left no doubts on The Pearl circuit. The American set the fastest intermediate times in all sections to finish the 28.9 km course in 34min 42sec, riding close to 50 kilometres per hour.
“I’m from Arizona, so I’m used to the heat. I conserved my energy initially and started pushing hard from the 10th minute. From then on, it was all or nothing for me. I’m so glad I won,” McNulty said.