Filippo Inzaghi's side were second best for much of the match at Stadio Sant'Elia on Wednesday and fell behind to Victor Ibarbo's 24th-minute header.
But Bonaventura handed Milan a lifeline 10 minutes later when he caught out Cagliari goalkeeper Alessio Cragno with a superb distance effort - although after the match ended 1-1, the midfielder conceded it was something of a fluke.
"I was lucky, but they are things that happen over the course of a career," Bonaventura told Milan's official website.
"I'm happy. I went for it, it paid off. I tried to play the ball in the area and I found the back of the net."
Nether side could find a second goal, although Daniele Conti rattled Milan's post in the second half with a powerful free-kick before Diego Farias wasted a gilt-edged opening late on.
Milan were lucky to escape with a point, their second 1-1 draw in five days, and as a result dropped further off the pace of the top two - Juventus and Roma - in Serie A.
But Bonaventura felt most teams would have struggled against Cagliari, who came into the game full of confidence following a 4-0 away win over Empoli.
"Cagliari are a very organised side, they play well." added the 25-year-old.
"It wasn't a brilliant performance by us, but credit to the others that did well, we picked up a point, but we have to do more.
"Winning today against Cagliari would have been difficult for anybody, as they had an excellent match.
"We suffered in the first half, we tried to control the match, but their forwards put us in difficulty and forced us back in defence, which is not what we want."
