Norway's Tobias Halland Johannessen of Uno-X was three seconds behind Van Aert in second, while Australian Damien Howson (Q36.5), with the same time, was third.
American Magnus Sheffield (Ineos Grenadiers) was fourth overall, also at three seconds behind.
Van Aert, who also won the 2021 Tour of Britain, said Sunday had not been an easy ride.
"No, not at all," he told ITV. "I have to thank all my team mates for the whole week but especially for today because when (Rodriguez) attacked with 50k to go, I really had a hard time and I thought it would not be possible to take the GC (general classification win)."
Rodriguez, of Ineos Grenadiers, started the stage 39 seconds down before attacking on the mountain climb of Bryn Du some 50 kilometres from the finish and then held off a chase to lead the rest of the way for a 10th-place overall finish.
Rodriguez, of Ineos Grenadiers, started the stage 39 seconds down before attacking on the mountain climb of Bryn Du some 50 kilometres from the finish and led the rest of the way.
"I had no idea (if I could win), I just had to try to believe in myself, give everything I had and try to do a time trial to the finish," Rodriguez said. "I just had to go as fast as possible to the finish. It was very difficult so I have to be happy."
Van Aert found himself leading the chase group after Rodriguez attacked, with no team mates around him.
"I just tried to focus on going as hard as possible to the top first, because the time you lose there is the most valuable," the Belgian said. "Coming over the top, I tried to get as soon as possible an overview of the situation and really quick I heard in the radar that guys were still coming back, so I tried to stay calm."
The 166.8 km stage was temporarily neutralised at the 83 km mark due to a motor vehicle collision on the course that was unrelated to the race.
Stage eight travelled from picturesque Margam Country Park to the finish line in the shadows of Caerphilly Castle in South Wales, with a gruelling double ascent of Caerphilly Mountain.
