First, チリソース”は”ありますか is more natural than チリソース”が”ありますか.

チリソースはありませんか vs チリソースはありますか:
The former sounds to me that it can be a little more polite and/or you may be expecting a negative answer.
For example,
Waiter/waitress: “We have tomato sauce, Italian, French.”
You: “チリソースはありませんか” since the waiter/waitress did not say Chili sauce. You can also say “チリソースはないですか; a little less polite. ”The literal translation in English is “Don’t you have Chili sauce?”.

チリソースはありますか (Do you have Chili sauce?)； this also works in this situation as the same with English.

When a waiter/waitress asks you “What sauce would you like?”,
in this case, you can say “チリソースはありますか” just as a simple question. But ありませんか is also fine especially when チリソース can be a quite RARE sauce for the food you are ordering and you are expecting a negative answer.

Judging from this sentence, 

「チリソースはありますか？」

You may be in a restaurant and ask waiter , " Do you have Chili sauce ?"

「チリソースがありますか？」

waiter "yes , we have"

but you count hear well, and  confirm to say " Do you have Chili sauce?"

 In japanese, you know 「は」「が」have many meanings.

in your sentence, both are almost same, I think.