A supporter targeted Constant during the second half of the clash at Stadio Atleti Azzurri d'Italia, an action which drew sarcastic applause from team-mates Philippe Mexes and Nigel de Jong.
Milan coach Seedorf was quick to praise his players for not allowing the unsavoury incident to affect their performance on the pitch.
"I can only compliment my lads because they continued playing," Seedorf told Sky Sport Italia .
"I don't need to comment on the rest. Constant and his team-mates reacted in the best way by carrying on with their work."
A stunning last-gasp winner from Franco Brienza gave Atalanta three points after German Denis' penalty had cancelled out Milan's opener, which came courtesy of an own goal from Gianpaolo Bellini.
The defeat dents Milan's hopes of securing Europa League football for next season.
Yet Seedorf, whose future has been the subject of speculation, remains hopeful of gaining qualification for Europe's second-tier club competition and insists that his conscience is clear regarding his own performance since taking charge in January.
"This is a heavy defeat, as we had come here to win," he added.
"We did well in the second half, but Franco Brienza's goal was stunning. Just a minute earlier we had almost scored with Mario Balotelli (who hit the post) and deserved to net a second goal.
"There is certainly still hope for Europe because until a few months ago it had seemed impossible. Now we are battling.
"I do not evaluate, I just think about finishing the season as best we can with this group. There will be time for the rest.
"I am giving my all, so my conscience is clear. I am concentrated on the final game."