The former Italy goalkeeper, 56, replaced Kenny Jackett on 30 July, shortly after Chinese conglomerate Fosun International bought the club.
Despite significant investment in the playing squad in August, Wolves have won only four of 14 league games and are 18th in the Championship.
Zenga's assistant, Stefano Cusin, has also left Molineux.
First-team coach Rob Edwards has been placed in temporary charge and will prepare the team for Saturday's game at Blackburn.
A 1-0 home defeat by Leeds on 22 October was Wolves' fourth loss in five league matches, although midfielder Dave Edwards told BBC WM 95.6 after the game that Zenga retained the backing of his playing squad.
Nine Championship clubs appointed new managers before the start of the 2016-17 season, but Zenga's departure from Wolves means only four of them remain in their posts.
Roberto di Matteo, Paul Trollope, Nigel Pearson and Alan Stubbs left Aston Villa, Cardiff, Derby and Rotherham respectively in October.
Rob Gurney, BBC WM 95.6
The cut-throat, "success yesterday" culture of football in the modern era is perfectly illustrated here, with Zenga given less than three months to prove himself.
His training methods were clearly popular with the players, but equally some of his personnel decisions were deemed curious.
Integrating a huge number of new players, however technically proficient, was not going to be easy, but owners Fosun have decided that someone else can do better in the pursuit of the boundless riches of the Premier League.
Zenga's passion and commitment was clear. He was often an adversarial interviewee, steadfastly believing that he was right and the inquisitor was wrong.
Ultimately his employers decided he was wrong. And so to the next…
Championship club Wolves have parted company with head coach Walter Zenga after just 87 days in charge.