Imperial made the first run midway through the second quarter as Danny Jones got momentum shifting in the Tigers' direction with four consecutive points that put his team up 21-16.
Andres Quesada then got things going for Holtville when he hit a basket. Cueto added a layup and the Vikings managed to end the half trailing 21-20.
Holtville's turn at a run came with 3:40 in the third quarter with two Cueto free throws to put the Vikings down 30-25. Cueto added two more free throws and Jon Singh hit from outside the three-point arc to tie the game at 30-30.
Quesada, Jacob Freeman and Singh added scores to build a lead and complete a 15-point run.
Matt Taylor put an end to the Tiger scoring drought with a buzzer-beating three-pointer to end the quarter with Imperial trailing 38-33.
Taylor and Jones regained control for Imperial, scoring 10 unanswered points in the first two minutes of the final period.
Alex Martinez and Freeman pulled the Vikings to within one with just over four minutes to go and it was a seesaw battle until Cueto's appearance at the line. Taylor sank a desperation three-pointer as time expired, but Holtville walked off the court with the win.
"We knew Imperial would play us tough," said Holtville coach Mike Goodsell. "There's a lot on the line between Holtville and Imperial."
Goodsell commended the play of Imperial's Jones and Taylor.
"(Jones) hustles so much." Goodsell said. "It was kind of a battle between him and Cueto as to who was going to own the boards."
Goodsell said he is looking forward to the Vikings' match-up with Imperial later this season.
"I expect it will be just as tough if not tougher," Goodsell said. "We enjoy the competition. I just love going to Imperial."
On Saturday, Jon Singh scored 21 points as Holtville downed Antelope High of Wellton, Ariz., 52-48 at home. Eric Cueto added 15 points and Andres Quesada chipped in 13 for the Vikings (8-6 overall).
Holtville (2-1 IVL) next plays at Calexico at 7 p.m. Tuesday while Imperial (1-1) will host Southwest at 7 p.m. Tuesday.