Midfielder Granit Xhaka scored the only goal in a 1-0 win over Kaiserslautern, with Leverkusen down to 10 men for more than half the match.
Alonso's first full season managing at the top level finished with a Bundesliga and German Cup double, a Europa League final - and a stunning record of just one loss in 53 games.
Leverkusen's only loss came in Wednesday's Europa League final against Serie A side Atalanta, but Alonso's charges rebounded in dogged fashion.
"I need a bit more time to grasp it. It was a dream season. To be able to celebrate here is incredible - we need to enjoy it," Alonso told Germany's ARD network.
The coach, who rejected reported interest from Liverpool, Bayern Munich and Real Madrid to stay at Leverkusen this season, was serenaded with chants of "Xabi Alonso" by delirious fans whose club had only won two trophies before this season.
"Of course I'm happy but I'm especially proud of the players. The double is totally deserved."
The victory tested Alonso as he rarely has been this season, with Leverkusen reduced to 10 men late in the first half after centre-back Odilon Kossounou's second yellow.
Pictured cradling his head in his hands on the bench moments after, the 42-year-old took off striker Patrik Schick and winger Jonas Hofmann while his team sat deeper and attacked on the counter.
Despite their one-man advantage, Kaiserslautern were kept in check by the German champions, with few clear-cut chances in the second half.
"We quickly analysed who we can change," the coach.
"We played well and created some good chances, but what's most important was the belief of the team.
"They were ready to fight with 10 men and get it done."
Leverkusen join Bayern, Dortmund, Bremen, Cologne and Schalke as clubs to have won the German double.
Alonso, a two-time Champions League winner as a player, will return to the top European competition with Leverkusen next season, when the final is to take place at Munich's Allianz Arena.
"I'm not thinking about next season," the coach laughed.
"Holiday, holiday. Maybe after a week, but we're going to enjoy and celebrate this."
Leverkusen have a trophy parade planned through the city for Sunday.