Boyé's treble was added to by further goals from Mariano and former Osasuna man Pablo Ibáñez, while Ante Budimir scored twice in reply for the visitors. The result took Alavés to ten points from four matches and kept alive their perfect record at Mendizorroza this season.
Osasuna boss Luis Miguel Ramis did not shy away from the scale of his side's defensive collapse.
"Looking at where the goals came from, it might even be a deserved result," he said. "We made too many mistakes, especially in areas of the pitch where we need to be more decisive, and that ends up costing you in the top flight.
"The feeling we had was that we could have competed in this game even having gone 2-0 down."
Ramis broke down each goal individually, including the costly error from his own centre-back.
"The second is a mistake that can happen and doesn't normally happen to Alejandro Catena," he said. "The third goal, yes, is a great strike, but it comes from a throw-in where we didn't press and left a player unmarked, who on top of that is a forward who needed more attention.
"In the end we conceded two poor deliveries from wide areas, where we didn't compete for the ball, where we didn't track our man, and the opponent took advantage. We left too many gifts for a rival that is very strong in that type of situation."
The Osasuna coach, whose sides are typically known for defensive solidity, insisted the display was an aberration rather than a trend.
"We'll get that solidity back," he said. "Maybe all the mistakes we should make across 15 matchdays came together in one game. This serves to bring us back down to earth, if anyone had got carried away, and to know that tomorrow we have to keep working to prepare for the Espanyol game."
Sánchez Flores, by contrast, could barely contain his delight after another home win.
"There are few complaints you can make about that win. We'd have liked to defend the box a little better for their goal, but we were very active, with identity, with a lot of energy, creating chances, scoring beautiful goals and enjoying it with our fans," he said. "It's a wonderful day. When you work hard, all the reward comes on days like today."
He also paid tribute to his in-form forwards.
"I'm delighted when the strikers are the ones scoring. It's important that lads like Toni Martínez, Mariano, Boyé and Mañas are getting goals because we depend on them a great deal," Sánchez Flores said.