She was beaten by local girl Heidi El Tabakh, 1-6, 6-3, 4-6 here on Sunday.
In a 56-player main draw, 44 were given direct entries, including the world's top 16 players.
Sania, who was 121 rungs above the Canadian in the world rankings at 74, had a tough time in the first qualifying round as well.
She struggled to win the first round against another Canadian Marie-Eve Pelletier Saturday, 2-6, 6-4, 6-2.
Sania began the second round by losing the first set tamely. She regained her poise somewhat in the second, though she had problems holding her serve.
Despite being broken twice, she managed to make it a set-all, only because she could attack the Canadian's weak second serve. In the decider, she had ample opportunities to sail through but could not clinch any of the five break points she forced.Whereas the local girl capitalised on the one break point she had to make her first WTA Tour event main draw after two hours of struggle.
El Tabakh El of Oakville, Ontario, defeated top-seeded Anastasia Pavlyuchenkova in the first round."I'm very satisfied," said El Tabakh, 22. "I did a lot better than I thought I would coming into the tournament. I knew (my opponents) were better ranked than I am so I had nothing to lose and I just went for it."
The other remaining Canadian in the qualifying draw, Sharon Fichman of Toronto, fell to Wickmayer of Belgium 6-3, 6-2.
Also through to the main draw are seasoned campaigners Julie Coin, Maria Kirilenko, and Maria Rybarikova.
Sania will play in the doubles with her new partner Francesca Schiavone of Italy and their first-round opponents are Akgul Amanmuradova of Uzbekistan and Alla Kudryavtseva of Russia.
Deccan Herald is on WhatsApp Channels | Join now for Breaking News & Editor's Picks