The 23-year-old, who is set to travel with the squad for their pre-season tour of Austria later this week, has signed a four-year deal at Elland Road.
Ekuban spent last season on loan at Albanian side FK Partizani, playing in the Champions League and Europa League, and netted 17 goals in 34 appearances.
Colchester will hand late fitness tests to Ryan Jackson and Brandon Comley prior to their clash with Yeovil.
Arsenal secured their place in the quarter-finals of the Europa League following their 3-1 defeat of AC Milan at the Emirates Stadium on Thursday.
Danny Welbeck scored twice against AC Milan to toast his England recall by sending Arsenal into the last eight of the Europa League.
Ipswich striker Joe Garner will not play again this season after it emerged he suffered a fractured skull against Sheffield United last week.