Aina played for 90 minutes while Ameobi, who missed Bolton’s last league game against Sheffield United on Saturday, made a return and also featured for 90 minutes.
The only goal of the game was scored by Gary Madine in the 20th minute.
The defeat means Hull have gone five straight games without a win in the Championship (three defeats, two draws).
Their last win in the Championship was a 6-1 home victory against Birmingham City on September 30, 2017.
Following the defeat to Bolton, Hull are now 21st on 24 points, one place above the relegation zone in the Championship table.