"The Waste Land" is a tricky compilation of Eliot's meanderings and responses to current events, mythology, and obscure texts.

When faced with a difficult analysis, it may be helpful to go through and do a literal reading/paraphrase of the text; this will often help elucidate deeper meanings as well. 

When the thunder is speaking--This is actually based on a Hindu fable about what thunder says when it rumbles “Datta, dayadhvam, damyata” (Give, sympathise, control)" (from Eliot's note for line 401) .  Eliot refers to the heart, which he has already referred to in lines 41 and 296.  The heart usually implies desire, and the reader observes on the next line that Eliot ponders the "awful daring of a moment's surrender" (line 403).   The poet adds that this moment cannot be retrieved by an age of prudence (caution or discretion). 

Let's compile what we know so far:  Eliot writes of giving (the thunder says to give), the heart pounding, a daring moment that cannot be taken back--and he brings it all together with the statement "by this, and this only, we have existed" (line 405).  The 'this' refers to the daring, heart pounding moment. 

Deeper reading of the text:  Eliot suggests that the only time humanity truly gives occurs in intercourse (read into: "blood shaking," awful daring of a moment's surrender," the idea of indiscretion). 

Keep in mind that Eliot also wrote about the other messages in the thunder besides giving, like sympathising and controlling.  He addresses those two facets in "What the Thunder Said" as well.