There are two things amalgamated in that idea.

1º By 1996, Yeltsin had all the reasons not to let the elections go in a way unfavorable to him. He was immensely unpopular (with the approval just about 5 percent) because of the economic recovery still nowhere to be seen, the war in Chechnya that has turned into a bloody quagmire, and the appalling levels of corruption. Besides, when he let the power crisis of the 1993 fester to an urban guerrilla level and then crushed it with the armed force, he has set the precedent of the Winner-Takes-All (including the losers' lives) political culture that is still destroying us from within. Therefore, he (and his inner circle) was pretty convinced that in the event of his loss at the elections, he won't probably remain free.

The President has enough tools to influence the voting. For instance, he has the constitutional power to rule by decree and can use the decrees for something like pork-barrelling, only on the national level. He has the large extra-budgetary funds at his disposition that can't be accounted for. He has at his disposition the Presidential Administration that is basically a parallel government that lacks even the weak accountability the nominal government has.

Besides, the communists were a scare enough that Yeltsin was able to enlist the support from the post-Soviet business tycoons a.k.a. 'the oligarchs' (pretty much every of them having benefitted from ties in the government, or the president's inner circle), and some local leaders who ensured good results in their jurisdictions with every imaginable method. The media (either directly controlled by the government or by the business tycoons) turned up almost exclusively pro-Yeltsin, too, spinning his image of the last barrier against the communist revanche.

As you can expect, the elections of 1996 were not only unfair, but highly irregular. To give an example, Chechnya has reported a 3,5:1 support for Yeltsin while still fresh from being brutally pacified (shortly before the election day, the rebel leader Yandarbiev has been flown to Moscow and signed a truce; it hasn't lasted long); yet another one are the railroad staff and their families all over the country voting in advance overwhelmingly for Yeltsin.

2º Now to the U.S. / IMF implementation.

Of course, neither would like to see Zyuganov winning the elections. The communists' rhetorics was confrontational to say the least, so they were afraid of Russia repudiating all of the post-1991 treaties (such as recognition of the post-Soviet states' in exchange for becoming the legal successor of the USSR and keeping all of the Soviet nuclear arms to itself), refusing to pay up on loans, and starting a new Cold War at best or a full-blown reconquest of the 'historically Russian lands' at worst - one can only guess how much of this was just rhetorics, but no one would have liked to try it. So the Western decision-makers were ready to turn the blind eye on Yeltsin's crimes just because he was the old, known, and amenable kind of evil.

By 1996, Russia was still heavily depending on foreign loans (mostly through the IMF structures), so these were used as a stick and carrot. You can argue that this was immoral, but this doesn't amount to the CIA operatives infiltrating the polling stations or the electoral commissions or the IMF telling to use their money to bribe the electors - they simply hadn't to.

TL;DR: the elections were rigged, the U.S. and the IMF had the motives to let Yeltsin win, but that was done without a covert intervention from their part.