Levy has secured a place at the top table of European clubs just five months after Spurs were one of the six Premier League clubs to quit the ECA after committing to join the failed European Super League.
Manchester United executive vice-chairman Ed Woodward stepped down from the ECA board then and there has been no Premier League club representative since.
Levy are Manchester City chief executive Ferran Soriano were expected to stand for the vacancy but Soriano pulled out before the vote.
The Tottenham chairman is reported to have won support from Premier League clubs including Manchester United, Liverpool and Arsenal.
Levy will be joined on the board by representatives from Inter Milan and Atletico Madrid.
The news of Levy’s election was confirmed on the second day of the ECA’s general assembly in Geneva.