The Brazilian, who came on at half-time in Bergamo, chested down Alessandro Nesta's ball and poked it in at the near post to score Milan's first goal in four games in all competitions.
Milan coach Leonardo will hope Ronaldinho's first of the campaign helps him cling to his job ahead of the two-week international break.
NEWS: Leonardo loses voice, but not job
The rookie boss was given a vote of confidence by chief executive Adriano Galliani after the 1-0 defeat at home to FC Zurich in the Champions League in midweek.
His side showed the same nerves against joint-bottom Atalanta, who took the lead midway through the first half when Simone Tiribocchi swept the ball home inside the box.
The hosts then had Ivan Radovanovic harshly sent off on 39 minutes for two bookings but Milan still laboured to find a goal.
Striker Alexandre Pato missed a glorious chance and later hit the bar before the inconsistent Ronaldinho netted.
The goal meant Leonardo could afford a sigh of relief but Napoli boss Roberto Donadoni is under increased pressure after a 2-1 defeat at injury-hit AS Roma.
Argentine forward Ezequiel Lavezzi opened the scoring for Napoli on 26 minutes after Roma had already made two substitutions including goalkeeper Julio Sergio.
LUCKY STRIKE
Francesco Totti hit back with one lucky strike and one expert finish before being injured himself but having to stay on the pitch with Roma having used their three changes.
Sampdoria drew 1-1 at home with promoted Parma to move level on points with leaders and champions Inter Milan, who beat Udinese 2-1 on Saturday thanks to Wesley Sneijder's injury-time strike.
Samp went in front through Giampaolo Pazzini's excellent header in the 23rd minute but Daniele Galloppa equalised with a well-worked goal on the half hour.
Unbeaten Juventus, joint third with Fiorentina who drew 0-0 with Lazio, can take the Serie A lead if they win at Palermo later.
Genoa are fifth after ruining Bologna's 100th anniversary party with a 3-1 away victory. In-form Chievo won 2-1 at Cagliari and bottom side Livorno drew 0-0 at Siena.
