Colapinto was caught up in Oliver Bearman's 308kph crash at Suzuka last Sunday, with the Haas driver swerving to avoid the Argentine's much slower car and hitting the barriers with a force of 50G.
Some online blamed the Alpine driver, and directed abuse towards him on social media.
Alpine, in a lengthy statement, condemned 'hateful messages' aimed at Colapinto as well as their former driver Ocon, who accepted blame for a clash with Colapinto in Shanghai last month.
"Esteban took full responsibility and apologised to Franco, actively seeking him out in the media pen and also apologising on social media. The resulting abuse that followed was not in the spirit of the sport and was an oversight not to call it out sooner," it said.
"Abuse of any kind to all drivers is unacceptable and it was especially disappointing that it comes from a minority of fans of the team towards a driver who has given so much to the team in the past and is a Grand Prix winner for Alpine."
Talk of Gasly being favoured 'completely unfounded'
With Formula 1 now on a break due to the cancellation of April races in Bahrain and Saudi Arabia as a result of conflict in the Gulf region, Alpine said they also wanted to address concern about their treatment of the drivers.
Gasly has scored 15 of Alpine's 16 points in three races so far this season, with Colapinto's lone point scored in China.
"Any questions about sabotage or not giving Franco the same car are completely unfounded, which is why the team felt the need to speak out," said Alpine.
"There might be times this year when pushing in the development race that upgrades come to one car first, which the team will communicate and be completely transparent about. That being said, the aim will always remain to bring upgrades to both cars where possible.
"It's absolutely not in the team's interests to not score points and any suggestion of self sabotage isn't conducive to that ultimate end goal... there's no withholding of information or keeping performance tricks hidden away."