The 25-year-old winger was linked with a move to the Russian club late in the transfer window, while his fellow countryman was thought to be heading towards White Hart Lane
The reigning Russian champions still managed to make a big splash in the market before the window closed by completing an €100 million combined double signing of Porto forward Hulk and Benfica midfielder Axel Witsel.
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"We really have been negotiating Nani and Moutinho, but Hulk and Witzel were top priorities," explained Zenit chief Maxim Mitrofanov.
"It must be understood that any transfer campaign is based on the list of players, ranked by priority."
Mitrofanov also stated that a move was possible for the Manchester United man until they spoke to the player and realised that his salary expectations were beyond even their resources.
"If Hulk had demanded €8m (£6.4m) to €10m (£8m) a year, these conditions would have been unacceptable for Zenit," Mitrofanov explained.
"The transfer of Nani failed mostly due to this reason, as he asked for an enormous salary and we would not pay him."
Nani has just two years remaining on his contract at Old Trafford, while Moutinho was reportedly just minutes away from completing a switch to Andre Villas-Boas' Tottenham Hotspur before the window closed.