At the same event in 2013, three people were killed and 260 injured when two bombs exploded near the finish line.
The sportswear giant admitted its choice of words had been "insensitive" and said it was "incredibly sorry" for sending the document.
At least two survivors from the attack four years ago are known to have participated in this year's race.
Adidas, the official sponsor of the Boston Marathon, sent out the marketing email which contained the subject line, "Congrats, you survived the Boston Marathon!"
It is thought all of the runners who signed up for the 26.2 mile (42km) race received the document.
It did not take long for the email to be shared via social media where it was widely criticised.
In a statement, Adidas said the annual race "is one of the most inspirational sporting events in the world" and a reminder "of the hope and resiliency of the running community".
Security checks were carried out before this year's race with police sniffer dogs and armed officers stationed throughout the course.
Image copyrightFBI HANDOUTImage captionDzhokhar Tsarnaev was sentenced to the death penalty in 2015 for his role in the Boston Marathon bombing
In 2015, Dzhokhar Tsarnaev was found guilty of being behind the attacks and was sentenced to the death penalty.
Tsarnaev and his elder brother, Tamerlan, planted bombs close to the finish line.
The older brother was killed in a shootout with police.
Dzhokar Tsarnaev, then 19, fled the same shootout but was captured a day later, after being found hiding in a boat in the backyard of a house nearby.
The brothers had been living in the Massachusetts town of Cambridge, home of the prestigious Harvard University.