The Nigeria forward, who has scored six league goals, has been sidelined since November with a thigh muscle injury.
"Yes. He is in the squad," Alonso told a press conference when asked whether Boniface could start on Saturday. His team will look to bounce back after Tuesday's 2-1 Champions League loss at Atletico Madrid.
In the league, however, Leverkusen, last season's domestic league and Cup winners, are enjoying a winning run and are in second place on 41 points, four behind leaders Bayern Munich.
They have won their last eight games in the league to remain Bayern's main title rivals, with third-placed Eintracht Frankfurt a further five points behind on 36.
"I have always said Bundesliga is the most important competition for us," Alonso said. "We are on a positive wave and we want to stay on it but it will be a tough game for us tomorrow playing away at Leipzig."
Leipzig are fifth on 31 points.
The Spaniard also hinted Leverkusen could be active in the January transfer window after injuries to Jeanuel Belocian and Martin Terrier ended both players' seasons.
"We have to be smart and take a smart decision," Alonso said. "After two serious injuries we have to be active."