It seems as though people seem to forget the main existence of what Yoga truly is. They have got caught up in the essence (such as the misconceptions of Yoga being an exercise) that they forgot the real meaning of it. Even those who claim (wittingly or unwittingly) to put the spirituality in Yoga have not seem to actually look for the root of what Yoga is. Well let's take a look at what it originally meant.
1820, from Hindi yoga, from Sanskrit yoga-s, literally "union, yoking" (with the Supreme Spirit), from PIE root *yeug- "to join"
So what are we trying to unite ourselves with? We are trying to unite with God, whom is inside ourselves, as said by Prophet Issa/Jesus (pbuh) in the Gospel of Thomas (the original teachings of Jesus).
So what about meditation? How does it connect with yoga? Let's look at the definition of meditation.
c.1200, "contemplation; devout preoccupation; devotions, prayer," from Old French meditacion "thought, reflection, study," and directly from Latin meditationem (nominative meditatio) "a thinking over, meditation," noun of action from past participle stem of meditari "to meditate, think over, reflect, consider," frequentative form from PIE root *med- "to measure, limit, consider, advise, take appropriate measures" (cf. Greek medesthai "think about," medon "ruler;" Latin modus "measure, manner," modestus "moderate," modernus "modern," mederi "to heal,"medicus "physician;" Sanskrit midiur "I judge, estimate;" Welsh meddwl "mind, thinking;" Gothic miton, Old English metan "to measure;" also see medical).
Meaning "discourse on a subject" is early 14c.; meaning "act of meditating, continuous calm thought upon some subject" is from late 14c. The Latin verb also had stronger senses: "plan, devise, practice, rehearse, study."
What meditation is is to contemplate on remembering God (Allah) as it says in Sura 2:198, 2:200, 2:203, and so on. It's through prayer and devotions that connect with Allah.