The 25-year-old Bedene, ranked as low as 156, shocked his Spaniard opponent 3-6 6-3 7-6 (8) in a marathon and intense semifinal that lasted two hours and 42 minutes.
It will be Beden's first ever appearance in an ATP Tour singles final and the Slovenian has also become the first qualifier in the 20-year history of Chennai Open to reach the summit clash.
The two finalists had contrasting routes to the final as the Swiss had an easy passage in his title defence.
And it has been a dream run in the USD 450,000 tournament for Beden as he had also upset second seed Feliciano Lopez and fifth seed Guillermo Garcia-Lopez in previous rounds.
"I have worked very hard and it paid today. I wanted to win the semi-final, having lost on two occasions. I am happy with the way I won against Agut today in our first meeting," an elated Beden said after the match.
Agut could have closed the match in the 10th game of the third set, but Beden refused to give an inch and not only saved that game, but went on to stretch the match to a tie-breaker which he sealed after a very tight battle.
In the Wawrinka-Goffin clash, the Swiss saved seven of the 10 break chances on his serve while he broke his rival thrice in the match.
Capitalising on the only break in the first set, Wawrinka nosed ahead in the match and was up 2-0 in the second with an early break, but Goffin struck back.
Wawrinka, though, will have to play at his best to stop a marauding Bedene. It will be interesting to see how Bedene copes with the fatigue, having played some gruelling matches and that too after coming off the qualifiers.
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