The BMC rider was on Tuesday accosted by two men who demanded he hand over his team issue BMC teammachine SLR01.
One of the assailants was carrying a knife and Atapuma suffered a cut on his left hand and wrist during a struggle in which he refused to hand over the bike.
"It was a stressful event and I was lucky the police were able to get the two guys," said Atapuma.
BMC's chief medical officer Dr Max Testa said Atapuma now has a protective cast on his arm and will have to ride indoors the next ten days.
BMC said the injuries are not expected to affect Atapuma's racing program, which begins at the Tour Mediterraneen in France in February.
He is scheduled to return to Europe in a few weeks to attend a training camp in Spain.
"Darwin is in good spirits, but a little disappointed because the training was going well," said Testa. "The day before he was attacked, he did a five-hour mountain bike ride."
The assailants were later apprehended by police.
Like many of generation, Atapuma is a highly regarded Colombian talent with a climbing ability similar to the recent cohort of riders coming from that country.
In his 2014 career debut at the Tour de France he was tasked with riding in support of team mate Tejay van Garderen in the high mountains.
However he abandoned the race after he broke his left leg in a crash on Stage 7. The injury forced him to take the rest of the season off to recover.