In the early 90's, when living in Jakarta, I did multiple one day visits from Jakarta, starting with early morning [eg 6:30 am]flight to Yogyakarta, have local tour guide pick up our group at airport, visit Borobodur and outlying areas, drive back to town for 'city tour' and then fly back on late afternoon flight. So a one day visit is doable. But I would strongly suggest you arrange for a local English speaking tour guide and car/bus tour....back in the 90's it cost about US$100, regardless of number of people in the group.

On the other hand, the above is for friends/biz clients with limited time. I did the visit with a golf bag in hand and prefer a more leisurely schedule from Jakarta to Bali with stops along the way.

And there are those who swear to get to Borobodur to see the sun rise [or set], in which case your itinerary makes it a difficult proposition.

YMMV.