The question about just what was up with Hitler and Owens has come up before! I would direct you to /u/prufrock451's answer here in that thread, as well as my own response, which I'll repost here. The short of it is though that we can't say for sure, but evidence is not very strong:

Hitler didn't snub Owens specifically, but rather avoided congratulating (publicly) any athletes. During the opening day of the games, he met the German winner of an event (and a Finn too) to congratulate them and shake hands. He did in fact leave the stadium before the completion of a track and field event, which possibly is the origin of the "deliberate snub", but his departure was possibly timed with the elimination of the last German competitor in the high-jump that he had been there for. Owens was not racing at that time. However, it should be noted that Cornelius Johnson and David Albritton won gold and silver in the high jump, and were both African-American. So it is possible that Hitler left to snub black competitors, but it wasn't Owens. By the time Owens was racing Hitler had been chided by the IOC, who told him that it went against the spirit of the games to only congratulate some of the winners. If he was going to congratulate every German winner, it was only right that he would do so for every winner, regardless of their country of origin. So instead of doing the latter, he chose to congratulate no one^1 . By the time Owens won his first medal, this was Hitler's policy, so can't be taken as a specific snub.

Hitler seems to have known well enough to keep his feelings private, and according to Speer, was quite upset by Owens winning. He acknowledged that 'primitive man' might excel in certain physical attributes such as strength, but believed that this was an unfair advantage in competition, and all non-whites should be banned from future games. Further more, according to Baldur von Schirach, he stated the Americans should be "ashamed" that black men were winning their medals, and stated that he never would have shaken hands with any of them. When Schirach made the mistake of suggesting Hitler take a photo with Owens, Hitler "exploded in rage". Apparently later in life Owens told a reporter that Hitler did, in fact, pose for that picture, but it has never surfaced. (and also that report is from the Daily Mail, so...)

So the sum of it is that Hitler didn't go out of his way to snub Jessie Owens. But had it not been his policy by the time Owens won, his private behavior points to the fact that he would have, but in the end, everything is relying on recollections that might be faulty. What we can say with absolute certainty is that the racial policy of Nazi Germany, concerned with the racial hygiene of the "Aryans", was absolutely disposed against those of African ancestry

Third Reich in Power - Richard J. Evans

Hitler, 1936-1945: Nemesis - Ian Kershaw

By the Sword - Richard Cohen

^1 ^Or ^rather, ^instead ^of ^doing ^it ^publicly ^for ^the ^media, ^he ^continued ^to ^congratulate ^them ^but ^only ^in ^private. ^As ^an ^interesting ^aside, ^while ^I ^know ^that ^he ^did ^shake ^hands ^with ^her ^prior ^to ^the ^games, ^at ^a ^reception ^for ^the ^German ^team, ^I ^can't ^find ^whether ^he ^congratulated ^Helene ^Mayer ^after ^she ^took ^silver ^in ^Women's ^Foil. ^She ^was ^one ^of ^the ^few ^token ^Jews ^included ^on ^the ^German ^team, ^only ^after ^strong ^international ^pressure, ^and ^not ^without ^irony ^as ^her ^family ^had ^left ^Germany ^in ^1933. ^Heydrich ^did, ^however, ^call ^her ^a ^*"Jewish ^cunt"* ^to ^her ^face ^for ^losing ^the ^gold ^medal ^match ^(Against ^an ^Hungarian ^Jew). ^Whether ^or ^not ^Hitler ^contacted ^her, ^she ^did ^invite ^controversy ^by ^giving ^the ^Nazi ^salute ^on ^the ^podium ^(as ^required ^by ^the ^party ^for ^all ^German ^medalists)

I would think that yes Hitler did acknowledge Jesse Owens, as to whether he shook hands with him is highly debatable, but if logic means anything Hitler then understood the physical superiority of the African American people and as a result despite the his belief in the racial superiority of the third reich and the aryans realized that while he can't admit publicly the superior athleticism of the African people he knew that the were and probably thought that instead of ethnically cleansing the African people there might be a way for them to integrate into the third reich if not for study but to increase the ability of his soldiers, perhaps even leverage their athleticism to his own benefit.

For all it's worth Hitler was no fool, and had to realize that the African's/Blacks were far more physically capable and this valuable to his war effort, though he would make sure they were second class citizens he wouldn't commit genocide against them in hopes of learning why they were so physically superior and leverage to help him win the war if only to protect the German citizenry and his grand plan.