Jones' victory over Republican candidate Roy Moore means that Jones will replace incumbent GOP Sen. Luther Strange early next year.
For the immediate challenges ahead, such as taxes and government funding, McConnell's calculus remains about the same because he is trying to finish both of those critical issues before the end of the year.
The Kentucky Republican said Tuesday that Strange will serve out the rest of the session, so Jones probably won't be sworn in until at least January 3
. That means that for the next few weeks, McConnell will still command a 52-48 majority.
GOP tax negotiators -- busily hammering out a final bill that can pass the House and the Senate -- say they have always been full speed ahead on tax reform, regardless of the special election's outcome.
"Our schedule was never predicated on this election -- either way," one senior Republican aide told CNN after Jones was projected to be the winner Tuesday evening.
For next year, when that margin will slip to 51-49, every Republican senator who is "on the fence" will have enormous new leverage on the issues they care about. Republican Sens. John McCain of Arizona, Jeff Flake of Arizona, Susan Collins of Maine, Lisa Murkowski of Alaska and others will be able to demand more from McConnell, House Republicans and President Donald Trump in any negotiations.
If Trump is serious about trying to take another shot at repealing the Affordable Care Act, his margins for doing so just got a lot tighter and he will have to give more to this group if he wants to pass it.
Republicans in the House will have to accept this new reality too, which won't be easy, especially for House Freedom Caucus members, who are already frustrated with giving in to the Senate.
McConnell and Trump also thought they would have significant leverage with the many Democrats from red states Trump won in 2016 who are up for re-election this cycle. But Trump's unorthodox style and undisciplined approach to governing have weakened him with that seemingly vulnerable group and left them stronger than expected. Jones' victory will buoy them too.
Overall, Democrats will be empowered and will likely demand more when it comes to spending issues and other priorities, such as what to do about recipients of the Deferred Action for Childhood Arrivals program, which Trump set to expire early next year
. The push by Democrats to get a DACA deal before the end of the year may soften as they consider the stronger leverage they will have next year.
In terms of the balance of power, Democrats still have to defend many more seats than Republicans do in 2018, making a Democratic takeover still a long shot. But then again, who thought Alabama would elect a Democrat Tuesday night?