The International Cycling Union (UCI) said on Thursday that its independent licensing panel let the Kazakhstan government-backed squad keep WorldTour status, which ensures entries to all top races.
The UCI asked its panel in February to strip the license after a critical audit of Astana's anti-doping work conducted by the Institute of Sport Sciences of the University of Lausanne (ISSUL).
Instead, Astana will be "subject to strict monitoring" through the season by the university, including at Nibali's planned defense of cycling's biggest prize in July.
"The license commission shall be able to re-open the proceedings if Astana Pro Team fails to respect one or several of the conditions imposed, or if new elements arise," the UCI said in a statement.
Reasons for the panel's decision "will be published in due course," it said.
Astana management responded in a statement saying it would continue to colloborate with the UCI as its focus returns to racing.
"Astana Pro Team is grateful to the License Commission for the opportunity to present the team’s commitment to observing the UCI’s ethical criteria," the team said.
"Astana Pro Team is committed to respecting all measures recommended by ISSUL, and to collaborate in the implementation of further measures that enhance our procedures above and beyond the UCI's minimum requirements.
"Our focus now returns to racing"
The team was put under scrutiny after two senior riders - Kazakh brothers Maxim and Valentin Iglinskiy - were caught using EPO last season, and three development team members tested positive for steroids.
Riders also allegedly contacted Italian doctor Michele Ferrari, who was banned from the sport in the Lance Armstrong case.
Nibali was not implicated.
The Astana case has been seen as a major test in the post-Lance Armstrong era of the new UCI leadership's toughness on doping.
"They won't get a second chance," UCI president Brian Cookson said of Astana's issues last year. "They have had too many second chances in the past, perhaps."
Astana manager Alexandre Vinokourov is a former Ferrari client, who served a two-year doping ban before winning the 2012 London Olympics road race.