The Real Madrid midfielder says the whole squad are supporting the defender as a dispute over an alleged stamp from the Barcelona man continues
Busquets appeared to step on Pepe's head during the Clasico encounter on March 23, although the Barcelona man has since insisted he "didn't touch" the Portugal international.
Pepe brandished Busquets "a liar" on Wednesday following his comments and Alonso has voiced his support for his Blancos team-mate.
"Pepe expressed his sentiments and we are behind him fully," Alonso told a press conference.
"If it had been the other way round, it would have been talked about a lot more. He is a key player for us."
Alonso played 90 minutes in Madrid's 3-0 win over Borussia Dortmund in Wednesday's Champions League quarter-final first leg, and the Spain international admits he would savour a "special kind of glamour" should they end their long wait for a 10th European crown.
"We're pleased with the result. There's still 90 minutes to go. We're happy but not relaxed.
"They [La Liga and Champions League] are both difficult competitions, it's hard to chose. The Champions League has a special kind of glamour, and it's a few years since we won it. It's not a question of choosing, but fighting."
Despite losing ground in the league title race to Atletico Madrid and Barcelona, Alonso was encouraged by Real's improvements on last year and revealed his excitement at the season's finale as they prepare to face Real Sociedad on Saturday.
The 32-year-old added: "We're going better in the league, but it's not a question of comparing, we have six exciting weeks with important games, we have some important players out too. Now it's the business end.
"Anoeta is always a tough place to go, people get right behind their side. It will be an intense game, we have to win."