The page of your site that you want to rank high in SEO should not be the same page that redirects to paypal. For example, if your site has a homepage, a products page and a generic "checkout" page (which directs to paypal for the purchase) then you want to rank high in search results for the first two and not the last one. Checkout and cart pages have no generic meaning since they end up different for each visitor, where as your home page and products page are pages whose information and content you want to appear as high as possible.
Your visitor's session duration is a site-wide metric and not a page only. So if they hit your homepage, then go to your product page and then proceed to a checkout page which directs to paypal you are safe compared to a scenario where they hit your homepage and immediately click an outbound link.
To sum it up, yes, low session duration affects your SEO. But you don't (shouldn't) want to score high SEO ranking for checkout/cart pages, actually you add noindex for pages like these so they are not followed at all (no reason to have your empty cart page appear on search results pages). If you focus on good SEO ranking for your homepage/products page your site will not be affected by a low SEO ranking for the one page that redirects to pay pal.
On the other side, is your site a single page application where the homepage is also the product page and at the same time the page from which the user gets redirected to paypal? If that is the case you will have more trouble getting a good SEO ranking and also your fears may be more valid as single page applications require some different architecture for getting a good SEO ranking. If this is indeed the case, you should give us more details, but even then, you can consider the usage of nofollow tag for the paypal redirection, a pop up window/modal for the purchase or something else that suits your case.